U.S. patent application number 16/419820 was filed with the patent office on 2019-11-14 for fluidic devices, systems, and methods for encapsulating and partitioning reagents, and applications of same.
The applicant listed for this patent is 10X Genomics, Inc.. Invention is credited to Rajiv Bharadwaj, Benjamin Hindson, Christopher Hindson, Anthony Makarewicz, Donald Masquelier, Debkishore Mitra, Kevin Ness, Serge Saxonov.
Application Number | 20190344276 16/419820 |
Document ID | / |
Family ID | 54264868 |
Filed Date | 2019-11-14 |
United States Patent
Application |
20190344276 |
Kind Code |
A1 |
Bharadwaj; Rajiv ; et
al. |
November 14, 2019 |
FLUIDIC DEVICES, SYSTEMS, AND METHODS FOR ENCAPSULATING AND
PARTITIONING REAGENTS, AND APPLICATIONS OF SAME
Abstract
The disclosure provides devices, systems and methods for the
generation of encapsulated reagents and the partitioning of
encapsulated reagents for use in subsequent analyses and/or
processing, such as in the field of biological analyses and
characterization.
Inventors: |
Bharadwaj; Rajiv;
(Pleasanton, CA) ; Ness; Kevin; (Pleasanton,
CA) ; Mitra; Debkishore; (Berkeley, CA) ;
Masquelier; Donald; (Tracy, CA) ; Makarewicz;
Anthony; (Livermore, CA) ; Hindson; Christopher;
(Pleasanton, CA) ; Hindson; Benjamin; (Pleasanton,
CA) ; Saxonov; Serge; (Oakland, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
10X Genomics, Inc. |
Pleasanton |
CA |
US |
|
|
Family ID: |
54264868 |
Appl. No.: |
16/419820 |
Filed: |
May 22, 2019 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15596754 |
May 16, 2017 |
10343166 |
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16419820 |
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14682952 |
Apr 9, 2015 |
9694361 |
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15596754 |
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61977804 |
Apr 10, 2014 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
B01L 3/502761 20130101;
G01N 35/085 20130101; B01L 2400/086 20130101; G01N 2035/1034
20130101; B01L 2200/0673 20130101; G01N 2035/00237 20130101; B01L
2300/0816 20130101; B01L 3/502784 20130101; B01L 2400/049 20130101;
B01L 3/0241 20130101 |
International
Class: |
B01L 3/00 20060101
B01L003/00; B01L 3/02 20060101 B01L003/02 |
Claims
1.-2. (canceled)
3. A device for generating a droplet comprising a single bead of a
plurality of beads, comprising: (i) a first channel connected to a
first end of a flow regulator, wherein said first channel is
configured to receive a first fluid comprising said plurality of
beads, wherein said beads of said first fluid flow at an irregular
frequency in said first channel; (ii) a droplet generation junction
configured to bring a second fluid that is immiscible with said
first fluid in contact with said first fluid; and (iii) a second
channel connected to a second end of said flow regulator and to
said droplet generation junction, wherein said flow regulator
comprises a broadened channel region at said first end and a
funneling channel region ending at said second end, wherein said
flow regulator is configured to (a) allow beads of said plurality
of beads from said first channel to gather in said broadened
channel region, and (b) allow said beads gathered in said broadened
channel region to flow through said funneling channel region and
into said second channel at a regular flow frequency, wherein said
second channel is configured to bring said beads in contact with
said second fluid to generate a droplet comprising said single bead
from said beads of said plurality of beads.
4. A microfluidic system, comprising: a first fluid source fluidly
connected to a first channel and comprising a first fluid that
comprises an aqueous fluid and a plurality of beads; a droplet
generation junction configured to bring said first fluid in contact
with a second fluid from a second fluid source, wherein said second
fluid is immiscible with said first fluid; a flow regulator fluidly
connected to the first channel and a second channel, wherein the
flow regulator (1) accepts beads from the plurality of beads from
the first channel and (2) provides the beads in the second channel,
wherein the flow regulator has a cross-section that is greater than
a cross-section of the first channel such that the beads flow at a
flow frequency that is substantially regular in the second channel
as determined by a number of beads that flow past a given point in
the second channel within a one second period of time; and a flow
control system that: (i) subjects the first fluid from the first
fluid source to flow along the first channel, through the flow
regulator, and into the second channel, such that the beads from
the plurality of beads flow at the flow frequency that is
substantially regular in the second channel as determined by the
number of beads that flow past the given point in the second
channel within the one second period of time, and (ii) subjects the
first fluid to flow along said second channel towards said droplet
generation junction, such that the beads and the second fluid meet
at the droplet generation junction to generate a plurality of
droplets comprising the beads from the plurality of beads.
5. A method for partitioning beads, comprising: (a) providing a
partitioning system comprising: (i) a first channel comprising a
plurality of filtering structures that is configured to receive a
first fluid comprising a plurality of beads, and (ii) a droplet
generation junction connected to the first channel, wherein the
droplet generation junction is configured to bring the first fluid
in contact with a second fluid that is immiscible with the first
fluid; and (b) in the partitioning system, (i) subjecting the first
fluid to flow along the first channel and through the plurality of
filtering structures such that the first fluid is filtered and
beads of the plurality of beads flow along the first channel to the
droplet generation junction, and (ii) at the droplet generation
junction, bringing the first fluid comprising the plurality of
beads in contact with the second fluid to generate a plurality of
droplets comprising the beads of the plurality of beads.
Description
CROSS-REFERENCE
[0001] This application is a continuation of U.S. application Ser.
No. 15/596,754, filed May 16, 2017, which is a continuation of U.S.
application Ser. No. 14/682,952, filed Apr. 9, 2015, which claims
priority to U.S. Provisional Application No. 61/977,804, filed Apr.
10, 2014, each of which is entirely incorporated herein by
reference for all purposes.
BACKGROUND
[0002] The field of life sciences has experienced dramatic
advancement over the last two decades. From the broad
commercialization of products that derive from recombinant
deoxyribonucleic acid (DNA) technology, to the simplification of
research, development and diagnostics, enabled by critical research
tools, such as the polymerase chain reaction, nucleic acid array
technologies, robust nucleic acid sequencing technologies, and more
recently, the development and commercialization of high throughput
next generation sequencing technologies. All of these improvements
have combined to advance the fields of biological research,
medicine, diagnostics, agricultural biotechnology, and myriad other
related fields by leaps and bounds.
[0003] None of these technologies generally exist in a vacuum, but
instead are integrated into a broader workflow that includes
upstream components of sample gathering and preparation, to the
downstream components of data gathering, deconvolution,
interpretation and ultimately exploitation. Further, each of these
advancements, while marking a big step forward for their fields,
has tended to expose critical bottlenecks in the workflows that
must, themselves, evolve to fit the demands of the field. For
example, genome sequencing is bounded on both ends by critical
workflow issues, including, in many cases, complex and labor
intensive sample preparation processes, just to be able to begin
sequencing nucleic acids from sample materials. Likewise, once
sequence data is obtained, there is a complex back-end informatics
requirement in order to deconvolve the sequence data into base
calls, and then assemble the determined base sequences into
contiguous sequence data, and ultimately align that sequence data
to whole genomes for a given organism.
[0004] One critical bottleneck for many of these technologies lies
not in their ability to generate massive amounts of data, but in
the ability to more specifically attribute that data to a portion
of a complex sample, or to a given sample among many multiplexed
samples.
SUMMARY
[0005] Devices, methods and systems of the present disclosure
provide solutions to challenges in various fields, including the
challenges described above. The present disclosure provides
devices, systems and methods for the generation of encapsulated
reagents as well as multiplexed partitions that include these
encapsulated reagents for use in a variety of applications.
[0006] The devices, systems and methods of the present disclosure
employ microfluidic systems in the generation of monodisperse
populations of microcapsules or beads that may have reagents such
as biological reagents associated therewith. Also provided are
devices, systems and methods for selectively and controllably
partitioning these microcapsules or beads into droplets in
emulsions for use in performing further reactions and/or analyses.
Also provided are the various component parts of the devices and
systems as well as interface components for facilitating
interaction between such components.
[0007] An aspect of the disclosure provides a method for
partitioning microcapsules. The method can include providing an
aqueous fluid comprising a suspension of microcapsules and flowing
the aqueous fluid into a droplet generation junction comprising a
partitioning fluid to form a population of droplets of the aqueous
fluid in the partitioning fluid. The flow rate of the aqueous fluid
can be such that no more than 50% of droplets of the population of
droplets are unoccupied by a microcapsule from the suspension of
microcapsules.
[0008] In some embodiments, the flow rate is such that no more than
25% of the droplets of the population of droplets are unoccupied by
a microcapsule. In some embodiments, the flow rate is such that no
more than 10% of the droplets of the population of droplets are
unoccupied by a microcapsule. In some embodiments, the flow rate is
such that no more than 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%,
5%, 2% or 1% of the population of droplets are unoccupied by a
microcapsule.
[0009] In some embodiments, fewer than 25% of droplets of the
population of droplets comprise more than one microcapsule. In some
embodiments, fewer than 20% of droplets of the population of
droplets comprise more than one microcapsule. In some embodiments,
fewer than 15% of droplets of the population of droplets comprise
more than one microcapsule. In some embodiments, fewer than 10% of
droplets of the population of droplets comprise more than one
microcapsule. In some embodiments, fewer than 5% of droplets of the
population of droplets comprise more than one microcapsule.
[0010] In some embodiments, at least 80% of droplets of the
population of droplets comprise a single microcapsule. In some
embodiments, at least 90% of droplets of the population of droplets
comprise a single microcapsule. In some embodiments, at least 95%
of droplets of the population of droplets comprise a single
microcapsule. In some embodiments, at least 70%, 75%, 80%, 85%,
90%, 95%, 98% or 99% of droplets of the population of droplets
comprise a single microcapsule.
[0011] In some embodiments, the droplet generation junction can be
in a microfluidic channel network of a microfluidic device. In some
embodiments, the microfluidic channel network can comprise a first
channel segment fluidly connecting a source of microcapsules to the
droplet generation junction. The microfluidic channel network can
also comprise a second channel segment connecting a source of
partitioning fluid to the droplet generation junction, and a third
channel segment fluidly connected to the droplet generation
junction providing an outlet to the droplet generation
junction.
[0012] In some embodiments, the flow rate can be provided by
providing one or more pressure differentials across the first and
second channel segments. In some embodiments, the first and/or
second channel segments can have cross-sectional dimensions that
provide the flow rate such that no more than 50% of droplets of the
population of droplets are unoccupied by a microcapsule from the
suspension of microcapsules. In some embodiments, the microfluidic
channel network can further comprise one or more flow controlling
structures within the first channel segment that provide the flow
rate.
[0013] In some embodiments, the microcapsules of the suspension of
microcapsules have a mean cross-sectional dimension and a
coefficient of variation in cross-sectional dimension of no greater
than 10%. In some embodiments, the microcapsules of the suspension
of microcapsules have a mean cross-sectional dimension and a
coefficient of variation in cross-sectional dimension of no greater
than 10%, 8%, 6%, 4%, 2% or 1%.
[0014] An additional aspect of the disclosure provides a method for
partitioning microcapsules. The method can include flowing an
aqueous fluid comprising a suspension of microcapsules into a
droplet generation junction comprising a partitioning fluid. During
a window of droplet generation, the microcapsules can be flowing
into the droplet generation junction at a frequency that varies
less than 30%. The method can also include partitioning the
microcapsules in the partitioning fluid during the window of
droplet generation. In some embodiments, the frequency is greater
than 50 Hz. In some embodiments, the frequency is greater than 500
Hz. In some embodiments, the frequency is greater than 1000 Hz. In
some embodiments, the frequency is greater than 50 Hz, 100 Hz, 250
Hz, 500 Hz, 750 Hz, 1000 Hz, 1250 Hz, 1500 Hz, 1750 Hz or 2000
Hz.
[0015] In some embodiments, during the window of droplet
generation, the microcapsules flow into the droplet generation
junction at a frequency that varies less than 20%. In some
embodiments, during the window of droplet generation, the
microcapsules flow into the droplet generation junction at a
frequency that varies less than 10%. In some embodiments, during
the window of droplet generation, the microcapsules flow into the
droplet generation junction at a frequency that varies less than
5%. In some embodiments, during the window of droplet generation,
the microcapsules flow in the droplet generation junction at a
frequency that varies less than 30%, 25%, 20%, 15%, 10%, 5%, 2% or
1%.
[0016] In some embodiments, flowing the aqueous fluid comprising
the suspension of microcapsules in the droplet generation junction
comprising a partitioning fluid can comprise flowing the aqueous
fluid through a microfluidic channel fluidly connected to the
droplet generation junction. The microfluidic channel can include a
region that regulates the flow (e.g., flow rate) of the
microcapsules.
[0017] An additional aspect of the disclosure provides a method for
producing microcapsules. The method can include providing a gel
precursor in an aqueous fluid and flowing the aqueous fluid having
the gel precursor through a fluid conduit that is fluidly connected
to a droplet generation junction comprising a partitioning fluid.
The partitioning fluid can comprise a gel activation agent. The
method can also include forming droplets of the aqueous fluid in
the partitioning fluid, where, within the droplets, the gel
activation agent contacts the gel precursor to form gel
microcapsules. In some embodiments, the aqueous fluid can also
comprise a biological molecule, where, for example, the biological
molecule can become entrained in the gel microcapsules.
[0018] An additional aspect of the disclosure provides a method for
partitioning microcapsules. The method can include flowing an
aqueous fluid comprising a suspension of a monodisperse population
of microcapsules into a droplet generation junction. The
monodisperse population can have a mean cross-sectional dimension
and a coefficient of variation in cross-sectional dimension of no
greater than 10%. The method can also include introducing a
partitioning fluid into the droplet generation junction and
separating the aqueous fluid into droplets within the partitioning
fluid, where the droplets contain one or more microcapsules.
[0019] An additional aspect of the disclosure provides a
microfluidic system. The microfluidic system can include a
microfluidic channel network comprising at least first, second and
third channel segments in fluid communication with a droplet
generation junction. The first channel segment can be fluidly
connected to a first fluid source that comprises a first fluid that
comprises an aqueous fluid. The aqueous fluid can comprise a
plurality of microcapsules disposed therein. Moreover, the second
channel segment can be fluidly connected to a second fluid source
that comprises a second fluid that is immiscible with the aqueous
fluid. The microfluidic system can also include a flow control
system connected to the microfluidic channel network. The flow
control system can subject the first fluid and second fluid to flow
into the droplet generation junction to generate droplets that
comprise microcapsules; and can subject the droplets to flow into
the third channel segment such that at least 75% of the droplets
comprise at least one microcapsule and fewer than 25% of the
droplets comprise more than one microcapsule.
[0020] An additional aspect of the disclosure provides a
microfluidic system. The microfluidic system can include a
microfluidic channel network. The microfluidic channel network can
comprise a first channel segment coupled to a source of a first
aqueous fluid that comprises a suspension of microcapsules; at
least one second channel segment coupled to a source of a second
aqueous fluid, the first and second channel segments in fluid
communication at a first junction that brings the first aqueous
fluid in contact with the second aqueous fluid; and a third channel
segment coupled to the first junction and intersecting at least one
fourth channel segment at a second junction. The at least one
fourth channel segment can be coupled to a source of a fluid that
is immiscible with the first and second aqueous fluids. Moreover,
the second junction can partition the first and second aqueous
fluids into droplets within the fluid. The microfluidic system can
also include a flow control system operably coupled to the
microfluidic channel network. The flow control system can subject
the first, second and third fluids to flow through the microfluidic
channel network to form droplets comprising the first and second
aqueous fluids in the fluid, at a frequency of at least 50 Hz and
that varies less than 20%.
[0021] Additional aspects and advantages of the present disclosure
will become readily apparent to those skilled in this art from the
following detailed description, wherein only illustrative
embodiments of the present disclosure are shown and described. As
will be realized, the present disclosure is capable of other and
different embodiments, and its several details are capable of
modifications in various obvious respects, all without departing
from the disclosure. Accordingly, the drawings and description are
to be regarded as illustrative in nature, and not as
restrictive.
INCORPORATION BY REFERENCE
[0022] All publications, patents, and patent applications mentioned
in this specification are herein incorporated by reference to the
same extent as if each individual publication, patent, or patent
application was specifically and individually indicated to be
incorporated by reference. To the extent publications and patents
or patent applications incorporated by reference contradict the
disclosure contained in the specification, the specification is
intended to supersede and/or take precedence over any such
contradictory material.
BRIEF DESCRIPTION OF THE DRAWINGS
[0023] FIGS. 1A, 1B and 1C provide schematic illustrations of
example partition or droplet generating fluidic channel
junctions.
[0024] FIG. 2 schematically illustrates a simple, example fluidic
channel architecture for partitioning microcapsules and other
fluids into droplets in a water-in-oil emulsion.
[0025] FIGS. 3A and 3B schematically illustrate an example fluid
channel architecture for partitioning encapsulated reagents into
droplets in an emulsion.
[0026] FIG. 4 schematically illustrates an example channel network
and microfluidic device useful in partitioning encapsulated
reagents.
[0027] FIG. 5 schematically illustrates a side view of an example
reservoir structure for enhancing manipulation of microcapsule
compositions within fluidic devices.
[0028] FIGS. 6A and 6B illustrates an example microcapsule flow
regulating structure.
[0029] FIGS. 7A and 7B schematically illustrates an example of
interfacing fluid containing vessels with a fluid reservoir on a
device.
DETAILED DESCRIPTION
I. General
[0030] The present disclosure provides devices, systems and methods
that are particularly useful in managing complex samples for
analysis using high throughput analytical systems, including, for
example, high throughput nucleic acid analysis systems, such as
nucleic acid arrays, nucleic acid sequencing systems, nucleic acid
amplification and quantitation systems, or the like. In particular,
the devices, systems and methods described herein are particularly
useful in providing encapsulated reagents or reagent systems, and
co-partitioning these reagents with sample components for further
reaction and/or analysis. This co-partitioning of reagents and
sample components can be used, for example, in reducing the
complexity of the sample material by segregating portions of the
sample to different partitions. Further, by also segregating
reagents, one can subject each sample portion to a different
reaction, including for example, the application of unique
identifiers to different sample components, e.g., attachment of a
discrete barcode or tagging reagents to the discrete sample
components.
[0031] Particularly elegant examples of these co-partitioning
approaches are described in Published International Patent
Application No. WO2014/028537, and U.S. patent application Ser. No.
14/104,650 (filed Dec. 12, 2013), Ser. No. 14/175,935 (filed Feb.
7, 2014), Ser. No. 14/175,973 (filed Feb. 7, 2014), and 61/937,344
(filed Feb. 7, 2014), the full disclosures of each of which are
incorporated herein by reference in their entirety for all
purposes.
[0032] By way of example, one particularly elegant approach
provides a polymer microcapsule composition that includes nucleic
acid barcode sequences bound to the microcapsule, where the
barcodes associated with a given microcapsule have substantially
the same sequence of nucleotides, but where different discrete
microcapsules will have different barcode sequences associated with
such microcapsules. Each of these microcapsules is then contacted
with a portion of a sample fluid, such as a sample fluid that
includes a template nucleic acid from a sample material. The
mixture of sample material including the template nucleic acid and
the microcapsule is then partitioned into a small volume, such as a
droplet in a water in oil emulsion, such that the microcapsule and
a portion of the sample material are contained within the same
droplet. In addition to controlling the droplet generation process
to provide a desired number of microcapsules in a given partition,
the sample material and emulsion process also may be controlled to
provide for a desired amount of sample material, e.g., sample
nucleic acid material, within each partition, e.g., to provide a
single template molecule or a desired level of genome coverage
within a given partition, or other desired level of sample
materials.
[0033] Within the partition, the barcode sequence is reacted with
the sample material, e.g., the template nucleic acid to effectively
tag the sample material or a portion thereof. For example, by
reacting the barcode sequence with the template, e.g., through
amplification of the template sequence using the barcode sequence
as an extension primer, one can effectively "attach" the barcode
sequence to the replicated or amplified template. Similarly,
replication of the extended primer produces a complement of the
template along with a complement to the barcode, again, effectively
attaching the barcode to the template. The presence or attachment
of the barcode sequence, or its complement, on or to the amplified
template molecule, or its complement, then allows some level of
attribution of sequence reads that include that barcode to the same
portion of sample material, e.g., the same template molecule or the
same sample components, that was originally allocated to that
partition.
[0034] In many cases, the molecule that includes the barcode
sequence or sequences may also include functional elements that are
used in subsequent processing of the amplified template sequences.
These functional sequences include, for example, primer sequences
(e.g., targeted or universal), primer recognition sequences,
sequences that can form secondary structures, either within the
sequence, or upon replication of the sequence, enrichment
sequences, e.g., that are used as affinity purification sequences,
immobilization sequences, probe sequences, reverse complement or
hairpin sequences, or any of a variety of other functional
sequences.
[0035] There are a wide variety of other high-value applications
for such partitioning and barcoding or tagging processes. The
present disclosure advantageously provides devices, systems and
methods that can greatly facilitate the generation of such
partitioned compositions or components thereof.
II. Fluidic Systems for Producing Encapsulated Reagents and
Partitioned Reactions
[0036] The present disclosure provides improved fluidic systems,
and particularly improved microfluidic systems, that are useful for
both the generation of encapsulated reagents, as well as in the
partitioning of those encapsulated reagents for use in subsequent
reactions and/or analyses. As used herein, microfluidic systems
typically denote fluidic systems that employ one or more fluid
conduits, channels, chambers, or the like that include one or more
interior cross-sectional dimensions, e.g., depth, length or width,
that are less than 1000 microns, less than 200 microns, less than
100 microns, and in some cases, less than about 50 microns, or even
less than about 20 microns. In some cases, one or more
cross-sectional dimensions may be about 20 microns or less or 10
microns or less. Typically, these microfluidic channels or chambers
will have at least one cross-sectional dimension of between about 1
and about 100 microns.
[0037] As will be appreciated, reference to encapsulated reagents
is not intended to limit the scope of such reagents to completely
enclosed capsules, but is intended to reflect any of a variety of
methods of associating reagents with a given particle, bead, or
other solid or semi-solid particle phase. In particular,
encapsulation generally refers to the entrainment or other
attachment, coupling, or association of a particular species with a
solid or semi-solid particle, bead, enclosure, partition or
droplet, and is not limited to compositions in which the species is
entirely or partially enclosed within a larger structure.
[0038] In some aspects, encapsulated reagents are associated with
microcapsules that are generally spherical in shape, although they
may be elongated, plug shaped, or otherwise vary in their specific
shape. In some cases, microcapsules will have one or more
cross-sectional dimensions that are less than 200 microns, less
than 150 microns, or less than about 100 microns. In some cases,
microcapsules of the present disclosure have one or more
cross-sectional dimensions that are between about 10 and about 200
microns, between about 20 and 150 microns, between about 30 and 125
microns, in many cases between about 40 and about 100 microns, and
still other cases, between about 50 and about 75 microns.
[0039] While the dimensions of the microcapsules can be an
important consideration, in many applications the variability in
those dimensions is also an important consideration. In particular,
for example, the transport of a microcapsule through a microfluidic
system can be significantly impacted by the size of that
microcapsule. For example simple flow resistance may be greater for
much larger microcapsules than for smaller microcapsules.
Similarly, propensity for clogging may be greater for larger
microcapsules than for smaller microcapsules. In either event, flow
rates of microcapsules through a microfluidic system may be greatly
impacted by the size of the microcapsule. Accordingly, in certain
aspects, the microcapsules of described herein, will be provided as
a population of microcapsules having substantially monodisperse
cross-sectional dimensions. In terms of cross-sectional dimensions,
the phrase substantially monodisperse refers to a population that
deviates (e.g., expressed as a coefficient of variation and stated
as a percentage) from the mean cross-sectional dimension by no more
than 50%, no more than 40%, no more than 30%, no more than 20%, or
in some cases, no more than 10%.
[0040] Whether in the context of generating microcapsules for use
in entrainment or encapsulation of reagents, or in the partitioning
of aqueous fluids within non-aqueous droplets, the devices and
systems of the present disclosure can employ a similar
architecture. In a simplified example, this architecture may
include a first channel segment that is fluidly connected to a
first junction that fluidly connects the first channel segment with
a second channel segment and a third channel segment. The second
channel segment delivers to the junction a second fluid that is
immiscible with the first aqueous fluid, such as an oil, that
allows for the formation of aqueous droplets within the stream of
immiscible fluid. This second fluid may be referred to herein as
the dispersion fluid, partitioning fluid or the like. The flow of
the first and second fluids through the junction and into the third
channel segment is controlled such that droplets of the first fluid
are dispensed into a flowing stream of the second fluid within the
third channel segment. A variety of modifications to this basic
structure are available to better control droplet formation and to
bring in additional fluid streams. As used herein, the control of
fluid flows encompasses both active control of fluid flows through
the application of greater or lesser driving forces to cause that
fluid flow. Additionally, flows may be controlled in whole or in
part, by controlling the flow characteristics of one or more of the
fluids and/or the conduits through which they are flowing. For
example, fluid flow may be controlled by providing higher flow
resistance within a conduit, e.g., through providing a higher
viscosity, narrower conduit dimension, or providing larger or
smaller microcapsules within a fluid stream, or any combination of
the foregoing. In some cases, control is imparted through several
of controlled driving force, controlled conduit dimensions, and
controlled fluid properties, e.g., viscosity or particle
composition.
[0041] FIG. 1A provides a schematic illustration of an exemplary
basic channel architecture for generating droplets in a channel. As
shown, first channel segment 102, second channel segment 104, third
channel segment 106 and fourth channel segment 108 are all provided
in fluid communication at first junction 110. FIG. 1B schematically
illustrates droplet formation within the channel architecture of
FIG. 1A.
[0042] As shown, a first aqueous fluid 112 is flowed through
channel segment 102 toward junction 110. A second fluid 114 that is
immiscible with the first fluid 112 is flowed into junction 110 via
each of channel segments 104 and 106, and into fourth channel
segment 108. As the aqueous first fluid 112 reaches the junction
110, it is pinched by the flow of the second fluid 114 from channel
segments 104 and 106, and individual droplets 116 of the aqueous
first fluid 112 are dispensed into fourth channel segment 108. In
some cases, a portion of the fourth channel segment 108 proximal to
the junction 110 may be provided with a reduced cross-section (not
shown) as compared to the junction and/or channel segments 102, 104
and 106 to facilitate droplet formation within the fourth channel
segment 108.
[0043] As discussed in greater detail below, additional channel
segments may be provided either upstream, downstream or both, of
junction 110, in any of channel segments 102, 104, 106 or 108, to
allow for the delivery of additional fluids into either the aqueous
first fluid stream in segment 102, e.g., additional reagents,
buffers, or the like, the partitioning fluid in segments 104 and/or
106, or the droplet containing stream in channel segment 108.
[0044] As will be appreciated, this basic channel architecture is
widely useful in both generation of microcapsules for encapsulation
of reagents, as well as in the ultimate partitioning of those
encapsulated regents with other materials.
[0045] In one particular example and with reference to FIGS. 1A and
1B, above, a first aqueous solution of polymer precursor material
may be transported along channel segment 102 into junction 110 as
the aqueous fluid 112, while a second fluid 114 that is immiscible
with the polymer precursor is delivered to the junction 110 from
channel segments 104 and 106 to create discrete droplets of the
polymer precursor material flowing into channel segment 108. In
some aspects, this second fluid 114 comprises an oil, such as a
fluorinated oil, that includes a fluorosurfactant for stabilizing
the resulting droplets, e.g., inhibiting subsequent coalescence of
the resulting droplets. Examples of particularly useful
partitioning fluids and fluorosurfactants are described for
example, in U.S. Patent Application No. 2010-0105112, the full
disclosure of which is hereby incorporated herein by reference in
its entirety for all purposes. Polymer precursor materials may
include one or more of polymerizable monomers, linear polymers, or
other
[0046] In preparing gel microcapsules, an activation agent may also
be combined with the aqueous stream 112 from channel 102. In some
aspects, this activation agent is disposed within the second fluid
streams 114 in one or more of channels 104 and 106, allowing for
the simultaneous formation of droplets and commencement of a
reaction to create the desired microcapsules 116. For example, in
the case where the polymer precursor material comprises a linear
polymer material, e.g., a linear polyacrylamide, PEG, or other
linear polymeric material, the activation agent may comprise a
cross-linking agent, or a chemical that activates a cross-linking
agent within the first stream. Likewise, for polymer precursors
that comprise polymerizable monomers, the activation agent may
comprise a polymerization initiator. For example, in certain cases,
where the polymer precursor comprises a mixture of acrylamide
monomer with a N,N'-bis-(acryloyl)cystamine (BAC) comonomer, an
agent such as tetraethylmethylenediamine (TEMED) may be provided
within the second fluid streams in channel segments 104 and 106,
which initiates the copolymerization of the acrylamide and BAC into
a cross-linked polymer network or, hydrogel.
[0047] Upon contact of the second fluid stream 114 with the first
fluid stream 112 at junction 110 in the formation of droplets, the
TEMED may diffuse from the second fluid 114 into the aqueous first
fluid 112 comprising the linear polyacrylamide, which will activate
the crosslinking of the polyacrylamide within the droplets,
resulting in the formation of the gel, e.g., hydrogel,
microcapsules 116, as solid or semi-solid beads or particles.
[0048] Although described in terms of polyacrylamide encapsulation,
other `activatable` encapsulation compositions may also be employed
in the context of the present disclosure. For example, formation of
alginate droplets followed by exposure to divalent metal ions,
e.g., Ca2+, can be used as an encapsulation process using the
described processes. Likewise, agarose droplets may also be
transformed into capsules through temperature based gelling, e.g.,
upon cooling, or the like.
[0049] In accordance with some aspects of the present disclosure
one or more reagents may be associated with the microcapsule at the
time of its formation. In particular, one or more reagents may be
associated with a precursor reagent to the polymer matrix that
makes up the microcapsule e.g., the linear polymer, such that the
reagent(s) will be entrained within or otherwise associated with
the formed microcapsule. For example, the reagent(s) may be coupled
to a linear polymer material that is cross-linked into a
microcapsule using the processes described herein, resulting in the
reagents being coupled to the formed and cross-linked gel
microcapsule. Alternatively, the reagent may be combined with the
polymer precursor that includes active binding sites that interact
with the reagent, either in the precursor stream or in the
microcapsule after formation. In still other aspects, as with the
cross-linking activation agent described elsewhere herein, an
activator may also be contacted with the polymer precursor or
formed microcapsule that activates sites on the polymer matrix of
the microcapsule to which the reagent components may associate,
covalently or non-covalently.
[0050] Reagents to be incorporated into the microcapsule may
include any of a variety of different reagents or other components
useful in the ultimate use of the microcapsule, e.g., an analytical
reaction. Such reagents may include labeling groups (e.g.,
fluorescent dye molecules, FRET pairs, fluorescent nanoparticles,
fluorescent proteins, mass labels, electrochemical labels or the
like). These reagents may include biological or biochemical
reagents, such as nucleic acids, nucleic acid analogues, nucleic
acid mimetics, polynucleotides or analogues, oligonucleotides or
analogues, enzymes, substrates, antibodies or antibody fragments,
antigens, epitopes, receptors, and receptor binding components,
proteins, polypeptides, amino acids, polysaccharides, or virtually
any type of biochemical reagent useful in any of a wide variety of
analyses. Likewise, compounds that act upon biological or
biochemical systems are also envisioned for inclusion in such
microcapsules, e.g., small molecule pharmaceutically active
compounds, radiological compounds, inhibitors and or initiators of
biological or biochemical compounds, chemical library compounds, or
the like. In certain examples, these reagents may include any of a
wide of variety of different reagents that are applicable to
desired reactions to be carried out within the ultimately created
partition, such as nucleic acid replication reagents (e.g.,
primers, polymerases, nucleotides or nucleotide analogues, buffers,
co-factors, or the like), specific binding groups (e.g., receptors,
antibodies or antibody fragments, binding peptides), or any other
reagents (e.g., enzymes, substrates, catalysts/initiators,
substrates, inhibitors, or the like).
[0051] In one example, a polynucleotide having an acrydite moiety
is provided within the aqueous fluid, where the polynucleotide is
coupled to the polymer precursor prior to its cross-linking into a
bead as described herein. This polynucleotide may comprise one or
more functional nucleic acid sequences, such as primer sequences,
attachment sequences, ligation sequences or barcode sequences. See,
e.g., U.S. Patent Application No. 61/937,344, which is entirely
incorporated herein by reference.
[0052] Once created, the microcapsules may be collected, e.g., from
a reservoir or other outlet at the end of channel segment 108. The
collected microcapsules may then be washed to remove crosslinking
agent, non-crosslinked polymer, emulsion oil and surfactant, any
other non-coupled reagents, out-sized microcapsules or portions
thereof, as well as any other contaminants imparted to the
microcapsules during their creation that may potentially interfere
with the use of the methods and systems described herein. In some
aspects, the microcapsules will comprise substantially pure
microcapsule compositions. By substantially pure microcapsule
compositions is meant that the monodisperse populations of
microcapsules, as described above, and their associated desired
buffer and reagents will make up at least 90% of the composition,
at least 95% of the composition, at least 99% of the composition,
and in many cases at least 99.9% of the composition. Once washed,
these microcapsules may be re-suspended in an aqueous solution,
e.g., a buffer and/or one or more selected reagents, for use in
subsequent processing. In accordance with the above, a variety of
different wash protocols may be used in series or in the
alternative in generating the substantially pure microcapsules
described above. By way of example, in some cases, the wash may
comprise a simple buffer exchange wash where the microcapsules are
separated from their supporting liquid, e.g., through settling,
centrifugation, filtration, or the like, and then re-suspended in a
new buffer solution that may or may not be the same buffer as was
originally containing the microcapsules. This type of wash may be
repeated multiple times to remove free contaminants from the
microcapsules. In alternative or additional wash steps, a more
stringent washing process may be employed to remove certain bound
species from the microcapsules. For example, where a microcapsule
comprises nucleic acid, protein or other associated reagents, a
denaturing wash step may be employed to remove additional bound
excess proteins, nucleic acids or the like. For example, in some
cases, the microcapsules may be washed with chaotropic agents, such
as urea, at elevated temperatures to remove other non-covalently
bound species, e.g., hybridized nucleic acids, etc. In still other
aspects, wash steps may be combined with extractive techniques, in
order to remove species that may be entrained within the interior
of the microcapsules. For example, in some cases, these extractive
processes may include electroelution, osmotic elution or other
techniques to draw non-covalently bound species from within
microcapsules.
[0053] In many cases, the substantially pure microcapsule
compositions are substantially free from aggregated microcapsules,
e.g., two, three, four or more microcapsules adhered together.
Separation of aggregated microcapsules may be carried out through a
variety of methods, including for example, size or flow based
separation techniques, e.g., filtration.
[0054] Although described with reference to the channel
architecture shown in FIGS. 1A and 1B, it will be appreciated that
variations of these structures and architectures may be practiced
within the scope of the present disclosure. For example, in some
cases, the interface of the aqueous stream with the partitioning
fluid may differ from the specific architectures described above.
In particular, as shown in FIG. 1A, the intersection of channel
segment 112 with channel segments 104 and 106 provides an interface
between the aqueous fluid flow in channel segment 102 and the
partitioning fluid. The droplets are formed as the aqueous fluid is
pushed into and through that interface into channel segment 108. In
some cases, however, the interface may be presented within an open
space or chamber or channel segment manifold within a fluidic
device, such that the interface exists as a "wall" of partitioning
fluid. An example of this type of droplet generation junction is
illustrated in FIG. 1C. As shown, a first channel segment 122 is
fluidly connected to a fluid manifold 132 that forms part of the
droplet generation junction. The manifold 132 is structured as a
larger open chamber, i.e., larger than the first channel segment,
with a droplet dispensing channel 134 exiting the manifold through
which formed droplets 138 are expelled through dispensing channel
or aperture 134 into channel segment 136. In some cases, additional
side channel segments 124 and 126 are also provided fluidly
connected to the manifold 132, as are channel segments 128 and 130.
In operation, a first aqueous fluid (e.g., the aqueous polymer
precursor fluid as described with reference to FIG. 1B, or the
microcapsule containing aqueous fluid described with reference to
FIG. 3B, below) is flowed into the manifold 132. An immiscible
fluid is introduced into the manifold through side channels 128 and
130. Within the manifold 132, the immiscible fluid forms an
interface that traverses the manifold 132 to the droplet dispensing
port (shown as the dashed lines extending from channel segments 128
and 130 to dispensing channel 134). In some cases, additional
aqueous fluids are introduced into the manifold through side
channels 124 and 126. As the fluids flow through the droplet
dispensing channel 134, the aggregate aqueous fluids, i.e., that
from channel segment 122 and in some cases from segments 124 and
126, are surrounded by the immiscible fluid from channel segments
128 and 130 and expelled through dispensing channel segment 134
into channel segment 136 as droplets 138 of aqueous fluids within
an immiscible fluid emulsion. As will be appreciated, controlling
the rate of droplet formation, as well as the relative volumes of
fluids combined in droplets within these types of structures is
accomplished through many of the same mechanisms described above
for basic channel intersections. In particular, controlled flow may
be achieved through a number of mechanisms, including, for example,
controlling the flow rates of the fluids being introduced into the
manifold, controlling the geometry of the channels as they enter
the manifold 132, e.g., channel shape, dimensions (depth and/or
width), intersection contours and structure, and setback from the
manifold as compared to other channels.
[0055] Additionally, although illustrated in FIG. 1A as a single
interface for droplet generation, it will be appreciated that the
devices and systems of the present disclosure will typically
comprise multiplexed droplet generating interfaces in order to
increase the throughput at which one can produce droplets for
microcapsule formation or for partitioning of microcapsules, as
described elsewhere herein. For example, a device or system of the
present disclosure may include multiple duplicate channel networks
of the architectures shown in FIGS. 1A and/or 1C. Further, for such
multiplexed devices or systems, some of the various channel
segments within the duplicate channel networks may have common
fluid sources in terms of a common reservoir or a common channel or
channel manifold, or may feed to a common outlet or reservoir.
Likewise, in the case of alternate architectures, multiple aqueous
fluid feed channel segments may be provided in communication with
the partitioning fluid chamber.
[0056] FIG. 2 schematically illustrates a microfluidic device or
device module for producing the microcapsules described above. As
shown, the microfluidic device typically includes a body structure
200 that includes within its interior portion, a channel network
that includes channels segments 202, 204, 206 and 208. These
channel segments all communicate with a common channel junction
210. The device body structure also includes reagent reservoirs 212
and 214. As shown, reagent reservoir 212 is fluidly coupled to
channel segment 202, while reagent reservoir 214 is fluidly coupled
to channel segments 204 and 206. A third outlet reservoir is shown
as reservoir 216, which is provided in fluid communication with
channel segment 208. As will be appreciated, the aqueous polymer
gel precursor may be provided in reservoir 212, while the
partitioning fluid and activating agent are provided in reservoir
214. Flow of these fluids through junction 210, creates the
microcapsules as described above, which flow into and are harvested
from reservoir 216.
[0057] These microfluidic devices or device modules may be
fabricated in any of a variety of conventional ways. For example,
in some cases the devices comprise layered structures, where a
first layer includes a planar surface into which is disposed a
series if channels or grooves that correspond to the channel
network in the finished device. A second layer includes a planar
surface on one side, and a series of reservoirs defined on the
opposing surface, where the reservoirs communicate as passages
through to the planar layer, such that when the planar surface of
the second layer is mated with the planar surface of the first
layer, the reservoirs defined in the second layer are positioned in
fluid communication with the termini of the channel segments on the
first layer. Alternatively, both the reservoirs and the connected
channel structures may be fabricated into a single part, where the
reservoirs are provided upon a first surface of the structure, with
the apertures of the reservoirs extending through to the opposing
surface of the structure. The channel network is fabricated as a
series of grooves and features in this second surface. A thin
laminating layer is then provided over the second surface to seal,
and provide the final wall of the channel network, and the bottom
surface of the reservoirs.
[0058] These layered structures may be fabricated in whole or in
part from polymeric materials, such as polyethylene or polyethylene
derivatives, such as cyclic olefin copolymers (COC),
polymethylmethacrylate (PMMA), polydimethylsiloxane (PDMS),
polycarbonate, polystyrene, polypropylene, or the like, or they may
be fabricated in whole or in part from inorganic materials, such as
silicon, or other silica based materials, e.g., glass, quartz,
fused silica, borosilicate glass, or the like.
[0059] Polymeric device components may be fabricated using any of a
number of processes including embossing techniques, micromachining,
e.g., laser machining, or in some aspects injection molding of the
layer components that include the defined channel structures as
well as other structures, e.g., reservoirs, integrated functional
components, etc. In some aspects, the structure comprising the
reservoirs and channel structures may be fabricated using, e.g.,
injection molding techniques to produce polymeric structures. In
such cases, a laminating layer may be adhered to the molded
structured part through readily available methods, including
thermal lamination, solvent based lamination, sonic welding, or the
like.
[0060] As will be appreciated, structures comprised of inorganic
materials also may be fabricated using known techniques. For
example, channel and other structures may be micro-machined into
surfaces or etched into the surfaces using standard
photolithographic techniques. In some aspects, the microfluidic
devices or components thereof may be fabricated using
three-dimensional printing techniques to fabricate the channel or
other structures of the devices and/or their discrete
components.
[0061] As noted previously, the above-described channel
architectures may also be readily employed in the partitioning of
the above described microcapsules, e.g., comprising the
encapsulated reagents, within droplets created in an immiscible
fluid, such as in a "water-in-oil" (WO) emulsion system, where an
aqueous solution, and particularly, an aqueous solution that
includes the encapsulated reagents described herein, is dispersed
as partitioned droplets within an immiscible dispersion or
partitioning fluid, such as an immiscible oil.
[0062] FIG. 3 schematically illustrates the partitioning of
encapsulated reagents. As shown, and with reference to the fluidic
architecture shown in FIG. 1A, a first aqueous fluid that includes
the beads encapsulating at least a first reagent is flowed through
channel segment 102 into channel junction 110. The dispersion fluid
is flowed into junction 110 from side channel segments 104 and 106.
The aqueous fluid is then partitioned into droplets within the
flowing stream of dispersion fluid, with individual droplets
including the encapsulated reagents, and in some cases, containing
only a single reagent bead or capsule.
[0063] The above-described channel architecture is included within
an example of a channel system shown in FIG. 3A, for partitioning
microcapsules, including, e.g., encapsulated reagents, with sample
materials into, for example, a water-in-oil emulsion system. As
shown, a first channel segment 302 is shown fluidly connected to
channel segments 304, 306 and 308 at first channel junction 310.
Fourth channel segment 308 fluidly connects first channel junction
310 to second channel junction 322 that is also fluidly coupled to
channel segments 324, 326 and 328.
[0064] In the context of partitioning encapsulated reagents, the
channel system of FIG. 3A is shown in FIG. 3B. As shown, a first
stream of a first aqueous fluid 312 containing microcapsules 350
(e.g., such as microcapsules prepared as described above), beads or
the like, that may include encapsulated reagents, are flowed
through channel segment 302 into channel junction 310. Additional
streams of second aqueous fluids 352 and 354 are introduced into
channel junction 310 from channel segments 304 and 306 to join the
first aqueous fluid 312 containing the microcapsules 350. The
aqueous fluids added through each of channel segments 304 and 306
may be the same as or different from each other and the fluid
portion of aqueous stream 312. As will be appreciated, the various
channel segments will typically be fluidly coupled to sources of
the fluids that are to be flowed through those channel segments.
Such fluid sources may include reservoirs integrated within a
device or interfaced with a device, or may include other interfaces
with other fluidic systems, e.g., syringes, pumps, fluidic networks
or the like, or interfaced with external reservoirs, e.g., external
fluid accession systems for drawing fluids from tubes, vials,
wells, or the like, or even external processing systems, e.g.,
amplification systems, sample material extraction systems,
filtration systems, separation systems, liquid chromatography
systems, or the like.
[0065] In some aspects, the additional aqueous fluids added through
side channels 304 and 306 may include sample materials that are to
be partitioned along with the encapsulated reagents included within
the microcapsules. For example, the second aqueous fluid may
include sample nucleic acids that may be partitioned into separate
droplets along with the reagents included with the microcapsules,
such as barcode sequences, functional sequences and the like.
Additional reagents may also be added in the second aqueous fluids.
In some cases, e.g., where the encapsulated reagents are to be
employed in nucleic acid replication or synthesis reactions, the
additional fluids may include reagents for such reactions, such as
DNA polymerase enzyme(s), primer sequences, nucleotides or
nucleotide analogues, reaction co-factors, buffers and the like, as
well as any of a variety of other reagents, e.g., dyes, labels,
chelators, inhibitors, initiators, substrates, etc.
[0066] In some cases, the reagents that are added may include
reagents that stimulate release of the encapsulated reagents into
the resulting droplets. For example, in some cases, the reagents
may be associated with the microcapsule through a disulfide linkage
or other chemically cleavable linkage, or the microcapsules may be
structurally held together by disulfide crosslinking, or other
chemically cleavable cross-linkers. As such, addition of a reducing
agent, such as dithiothreitol (DTT) can result in the eventual
release of the reagents on the microcapsules, either through direct
release or through dissolution of the microcapsule, or both (See,
e.g., U.S. Patent Application No. 61/940,318, filed Feb. 14, 2014,
the full disclosure of which is incorporated herein by reference in
its entirety for all purposes). Alternatively or additionally,
other cleavable linkages may be used to crosslink microcapsules.
Examples of such linkages include, e.g., photocleavable or
chemically cleavable linkages or cross-linkers.
[0067] The combined aqueous stream, e.g., from fluids 312, 352 and
354, flows through channel segment 308 into channel junction 322. A
third fluid 314 that is immiscible with the combined aqueous stream
flowing from channel segment 308 is introduced into channel
junction 312 from each of channel segments 324 and 326 to form
droplets 356 that include the microcapsules 350, as well as some
amount of the combined aqueous fluids. In many cases, this third,
immiscible fluid includes an oil, such as a fluorinated oil
containing a fluorosurfactant, as described above that is suitable
for forming water-in-oil emulsions with stabilized resulting
droplets. Other suitable emulsion systems may in some cases include
silicon and hydrocarbon oil/surfactant systems.
[0068] As alluded to above, the devices described herein are useful
in providing the microcapsules within aqueous droplets in an
immiscible fluid. As will be appreciated, in a number of
applications, it is particularly beneficial to provide a desired
level of microcapsule occupancy in created partitions. In general,
this is accomplished by controlling the combination of the aqueous
stream that includes the microcapsule, and the streams of the
immiscible fluid, such that the probability of more than the
desired number of microcapsules being incorporated into a given
partition is acceptably low. This may generally be accomplished
through control of the flow of microcapsules, along with the flow
of the other fluids coming together in the partitioning zone, e.g.,
junction 322 in FIG. 3, can be controlled so as to substantially
provide for a desired number of microcapsules per partition.
[0069] In many cases, the devices, systems and methods are used to
ensure that the substantial majority of occupied partitions (e.g.,
partitions containing one or more microcapsules) will include no
more than 1 microcapsule per occupied partition. In particular, in
some cases, the partitioning process is controlled such that fewer
than 50% of the occupied partitions contain more than one
microcapsule, fewer than 45% of the occupied partitions contain
more than one microcapsule, fewer than 40% of the occupied
partitions contain more than one microcapsule, fewer than 35% of
the occupied partitions contain more than one microcapsule, fewer
than 30% of the occupied partitions contain more than one
microcapsule, fewer than 25% of the occupied partitions contain
more than one microcapsule, and in many cases, fewer than 20% of
the occupied partitions have more than one microcapsule, while in
some cases, fewer than 10% or even fewer than 5% of the occupied
partitions will include more than one microcapsule per partition.
Accordingly, in many cases, the resulting partitions will result in
at least 50% of the partitions containing one and only one
microcapsule (i.e., a single microcapsule), at least 55% of the
partitions containing one and only one microcapsule, at least 60%
of the partitions containing one and only one microcapsule, at
least 65% of the partitions containing one and only one
microcapsule, at least 70% of the partitions containing one and
only one microcapsule, at least 75% of the partitions containing
one and only one microcapsule, at least 80% of the partitions
containing one and only one microcapsule, at least 80% of the
partitions containing one and only one microcapsule, at least 85%
of the partitions containing one and only one microcapsule at least
90% of the partitions containing one and only one microcapsule, and
in some cases at least 95% of the partitions containing one and
only one microcapsule.
[0070] Additionally or alternatively, in many cases, it is
desirable to avoid the creation of excessive numbers of empty
partitions. While this may be accomplished by providing sufficient
numbers of microcapsules into the partitioning zone, the poissonian
distribution can expectedly increase the number of partitions that
can include multiple microcapsules. As such, in accordance with
aspects of the present disclosure, the flow of one or more of the
microcapsules, or other fluids directed into the partitioning zone
are controlled such that, in many cases, no more than 50% of the
generated partitions will be unoccupied, i.e., including less than
1 microcapsule, no more than 25% of the generated partitions, or no
more than 10% of the generated partitions, will be unoccupied.
Further, in some aspects, these flows are controlled so as to
present non-poissonian distribution of single occupied partitions
while providing lower levels of unoccupied partitions. Restated, in
some aspects, the above noted ranges of unoccupied partitions will
be achieved while still providing any of the above-described single
occupancy rates described above. For example, in many cases, the
use of the devices, systems and methods of the present disclosure
creates resulting partitions that have multiple occupancy rates of
from less than 25%, less than 20%, less than 15%, less than 10%,
and in many cases, less than 5%, while having unoccupied partitions
of from less than 50%, less than 40%, less than 30%, less than 20%,
less than 10%, and in some cases, less than 5%. Methods, systems
and device configurations for controlling the various flows within
the channel networks are described in greater detail below.
[0071] Although described in terms of providing substantially
singly occupied partitions, above, in certain cases, it is
desirable to provide multiply occupied partitions, e.g., containing
two, three, four or more microcapsules within a single partition.
Accordingly, as noted above, the flow characteristics of the
microcapsule containing fluids and partitioning fluids may be
controlled to provide for such multiply occupied partitions. In
particular, the flow parameters may be controlled to provide a
desired occupancy rate at greater than 50% of the partitions,
greater than 75%, and in some case greater than 80%, 90%, 95%, or
higher.
[0072] Additionally, in many cases, the multiple microcapsules
within a single partition may comprise different reagents
encapsulated therein. In such cases, it may be advantageous to
introduce different microcapsules into a common channel or droplet
generation junction, from different microcapsule sources, i.e.,
containing different encapsulated reagents, through different
channel inlets into such common channel or droplet generation
junction. In such cases, the flow and frequency of the different
microcapsules into the channel or junction may be controlled to
provide for the desired ratio of microcapsules from each source,
while ensuring the desired pairing or combination of such
microcapsules into a partition.
[0073] Although shown with two junctions and their associated
channel segments, it will be understood that additional channels
may be provided within the devices of the present disclosure to
deliver additional components to the various fluids, capsules and
partitions described above. These additional channels may be
provided intersecting any of the various channel segments described
herein for addition of a variety of components to any one or more
of the various fluids flowing within those channel segments at
different positions and for different purposes. For example, in one
aspect, one or more additional side channels may be provided
intersecting the channel segment 328, described above, for the
purpose of introducing new fluids, reagents, or additional
partitioning fluids into partitioned fluids within the channel
segment 328.
[0074] Likewise, additional channel segments may be provided
intersecting channel segments 302 and/or 308, in order to introduce
additional fluids into the aqueous stream prior to separating that
fluid stream into droplets with the partitioning fluid.
Additionally, still other channel segments can be provided
intersecting any of the side channel segments, e.g., channel
segments 304, 306, 324, or 326, in order to deliver different
fluids into those channels. Such systems can allow the alteration
of fluids being introduced into the partitioning stream in real
time by controlling which fluids are provided through the
respective side channels, e.g., allowing one to change reactants,
change the partition fluid characteristics, or any of a variety of
other conditions.
[0075] In some cases, these additional fluids may be for purposes
of stimulating different reactions within the partitions by
introducing new reagents to the partitions. For example, these
additional fluids may provide one or more activating agents to the
partitions or capsules, that cause the initiation of one or more
reactions at any stage prior to or following partitioning.
[0076] Such activating agents may take any of a number different
forms. For example, these activation reagents may cause the release
of a reagent within a partition or capsule, to make it available
for reaction, e.g., by cleaving a linkage between a microcapsule
and the reagent, or by stimulating the disintegration of the
microcapsule and subsequent reagent release. Alternatively or
additionally, the activation reagent may comprise an initiator for
a desired reaction, such as a missing critical reagent for the
desired reaction, or the like. By way of example and for purposes
of illustration, in cases where the desired reaction includes a
nucleic acid polymerase mediated nucleic acid replication, an
activation reagent may include a key missing reagent, such as one
or more nucleoside triphosphates otherwise lacking from the
mixture, a primer sequence, or one or more reaction co-factors
suitable for a polymerase reaction, e.g., divalent metal ions like
magnesium or manganese. In many cases, the use of such missing
systems or activatable reagent systems for purposes of controlled
initiation of a given reaction are referred to as "hot start"
reagents, which are, as a general class, useful in conjunction with
the systems of the present disclosure.
[0077] The activation reagents may alternatively or additionally
initiate reactions on the partitions or capsules themselves or
both, for example, disrupting the capsules or releasing reagents
from those capsules, stabilizing or destabilizing partitions, e.g.,
to reduce or promote coalescence, respectively. A variety of
reagent systems may be employed in the disruption of or release of
reagents from the microcapsules of the present disclosure. These
include the use of chemical stimuli described above, for cleaving
chemical cross-linking or molecular attachment, as discussed in
U.S. Patent Publication No. 2014/0378345, which is entirely
incorporated herein by reference.
[0078] FIG. 4 provides a schematic illustration of an overall
exemplary microfluidic device or device module for partitioning
encapsulated reagents as described above. As shown in FIG. 4, the
overall device 400 provides one or more channel network modules 450
for generating partitioned microcapsule compositions. As shown, the
channel network module 450 includes a basic architecture similar to
that shown in FIG. 3B, above. In particular, the illustrated
channel network module includes a first channel junction 410
linking channel segments 402, 404 and 406, as well as channel
segment 408 that links first junction 410 to second channel
junction 422. Also linked to second junction 422 are channel
segments 424, 426 and 428.
[0079] As illustrated, channel segment 402 is also fluidly coupled
to reservoir 430 that provides, for example, a source of
microcapsules that may include one or more encapsulated reagents,
suspended in an aqueous solution. Each of channel segments 404 and
406 are similarly fluidly coupled to fluid reservoir 432, which may
provide for example, a source of sample material as well as other
reagents to be partitioned along with the microcapsules. As noted
previously, although illustrated as both channel segments 404 and
406 being coupled to the same reservoir 432, these channel segments
may be coupled to different reservoirs for introducing different
reagents or materials to be partitioned along with the
microcapsules.
[0080] Each of channel segments 402, 404 and 406 may be provided
with additional fluid control structures, such as passive fluid
valve 436. These valves may provide for controlled filling of the
overall devices by breaking the capillary forces that draw the
aqueous fluids into the device at the point of widening of the
channel segment in the valve structure. Briefly, aqueous fluids are
introduced first into the device in reservoirs 430 and 432, at
which point these fluids will be drawn by capillary action into
their respective channel segments. Upon reaching the valve
structure, the widened channel will break the capillary forces, and
fluid flow will stop until acted upon by outside forces, e.g.,
positive or negative pressures, driving the fluid into and through
the valve structure. Although illustrated as a widening of the
channel in the width dimension, it will be appreciated that a
passive valve structure may include a step up in any one or more
cross-sectional dimensions of a channel region. For example, a
passive valve may increase an increased stepped depth of a channel
at the valve region. Again, when the fluid reaches the increased
cross sectioned channel segment, the capillary forces will retain
the fluid within the shallower channel. Again, as noted, the
increase in cross-sectional dimension can be in any one or more
cross-sectional dimensions, and may be increases in cross section
of at least about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%
100%, or even more. In many cases, it may be between about 5% and
about 100% larger cross section, between about 5% and about 50%,
between about 5% and about 20% of an increase in cross section.
Although illustrated at a particular channel location, it will also
be appreciated that these valve structures may be positioned along
any channel location within a microfluidic channel network,
including at an intersection of two or more channel segments, or
within a singular channel.
[0081] Also shown in channel segment 402 is a microcapsule
funneling structure 452, that both allows the efficient gathering
of microcapsules from reservoir 430, regulation of microcapsule
flow (as described in greater detail elsewhere herein), as well as
reduced system failure due to channel clogging. As also shown, in
some cases, the connection of channel segment 402 with reservoir
430, as well as the junctions of one or more or all of the channel
segments and their respective reservoirs, may be provided with
additional functional elements, such as filtering structures 454,
e.g., pillars, posts, tortuous fluid paths, or other obstructive
structures to prevent unwanted particulate matter from entering or
proceeding through the channel segments.
[0082] Junction 410 is fluidly coupled to second junction 422. Also
coupled to channel junction 422 are channel segments 424 and 426
that are, in turn fluidly coupled to reservoir 438, which may
provide, for example, partitioning fluid that is immiscible with
the aqueous fluids flowing from junction 410. Again, channel
segments 424 and 426 are illustrated as being coupled to the same
reservoir 438, although they may be coupled to different
reservoirs, e.g., where each channel segment is desired to deliver
a different composition to junction 422, e.g., partitioning fluids
having different make up, including differing reagents, or the
like.
[0083] In exemplary operation, microcapsules provided in reservoir
430 are flowed through channel segment 402 into first channel
junction 410. The microcapsules will flow through valve 436, which,
in addition to providing a passive fluid valve structure also
operates as a microcapsule flow regulator, as described in greater
detail below. The microcapsule flow regulator ensures more regular
flow of microcapsules into and through junction 410 into channel
segment 408. Within junction 410, the aqueous microcapsule solution
is contacted with the aqueous fluids from reservoir 432, as
introduced by channel segments 404 and 406. Due to laminar flow
characteristics of the microfluidic channel networks, and without
being bound to any particular theory of operation, aqueous fluids
from channel segments 404 and 406 can ensheath the microcapsule
composition with a second aqueous fluid layer, where the primary
interaction between the two fluids is through simple diffusion,
i.e., with a substantial lack of convective mixing.
[0084] The aqueous fluid stream is then flowed through channel
segment 408 into second junction 422. Within channel junction 422,
the aqueous fluid stream, including the regularly spaced flowing
microcapsules, flowing through channel segment 408, is formed into
droplets within the immiscible partitioning fluid introduced from
channel segments 424 and 426. In some cases, one or both of the
partitioning junction, e.g., junction 422 and one or more of the
channel segments coupled to that junction, e.g., channel segments
408, 424, 426 and 428, may be further configured to optimize the
partitioning process at the junction.
[0085] Further, although illustrated as a cross channel
intersection at which aqueous fluids are flowed through channel
segment 408 into the partitioning junction 422 to be partitioned by
the immiscible fluids from channel segments 424 and 426, and flowed
into channel segment 428, as described elsewhere herein,
partitioning structure within a microfluidic device of the present
disclosure may comprise a number of different structures.
[0086] As described in greater detail elsewhere herein, the flow of
the microcapsules into junction 422, and in some cases the rate of
flow of the other aqueous fluids and/or partitioning fluid through
each of junctions 410 and 422, are controlled to provide for a
desired level of partitioning of microcapsules, e.g., to control
the number of microcapsules that will be partitioned in each
droplet, the amount of reagents in each droplet, and control the
overall operation of the device, e.g., to prevent clogging or other
disruption, or the like.
[0087] Once the microcapsules are partitioned, they are flowed
through channel segment 428 and into a recovery structure or zone
where they may be readily harvested. As shown, the recovery zone
includes, e.g., outlet reservoir 438. Alternatively, the recovery
zone may include any of a number of different interfaces, including
fluidic interfaces with tubes, wells, additional fluidic networks,
or the like. In some cases, where the recovery zone comprises an
outlet reservoir, the outlet reservoir will be structured to have a
volume that is greater than the expected volume of fluids flowing
into that reservoir. In its simplest sense, the outlet reservoir
may, in some cases, have a volume capacity that is equal to or
greater than the combined volume of the input reservoirs for the
system, e.g., reservoirs 430, 432 and 434.
[0088] As will be appreciated, a single microfluidic device may
include multiple substantially identical channel network modules
that may each have self-contained fluid sources or may share one or
more fluid reservoirs. For example, a single multiplexed device
including multiple channel network modules may include a single
source of one or more of the partitioning fluid, the microcapsule
containing fluid, one or more reagent fluids, as well as sample
fluids. As such, the multiple channel modules can be used to
generate large amounts of the same type of partitioned
microcapsules, e.g., by providing the same allocation of fluids in
the corresponding reservoirs of each module 450 in a multiplexed
device. In certain aspects, however, different channel network
modules will be used in the generation of different partitioned
microcapsules. Such different partitioned compositions may include
different sample materials being allocated to the partitioned
microcapsules, different initial microcapsules being allocated to
the same or different sample materials, or application of different
reagents to different to the same or different sample materials
and/or different microcapsules. As noted above, where the same
fluids are being introduced into the channel segments of different
modules, it can be efficient to have such channel segments fluidly
coupled to the same reservoir(s). These channel segments may be the
same corresponding channel segments in each module or, depending
upon the desired use, they may be different channel segments in
different modules.
[0089] As will be appreciated, the rates at which different fluids
are brought together in the channel structures described above can
have an impact on the generation of the droplets whether for the
purpose of microcapsule generation or for their subsequent
separation into discrete partitions or droplets. Accordingly, in
certain aspects, the devices used in the present disclosure provide
for control of the various fluid flows within the integrated
channel networks. Control of fluid flows within channel networks
may be accomplished through a variety of mechanisms. For example,
pressures may be applied at the origin of different channel
segments, e.g., on reservoirs, in order to control fluid flow
within that channel segment. By utilizing a pressure based flow,
one may be able to independently control flows within different
channel segments by coupling independently controlled pressure
sources to the different channel segments to apply differential
pressure gradients across each channel segment. In such cases, flow
rates within different channel segments may be monitored, e.g.,
through interfaced detection systems, such as optical detectors, to
provide feedback on the flow control aspects to allow modulation of
flow.
[0090] Alternatively, a single pressure source may be coupled to
all channel segments simultaneously, e.g., by coupling a pressure
source to a manifold that simultaneously connects to the various
channel segment origins or reservoirs. Where a single pressure is
applied over multiple channels, the flow rates within those
channels will be controlled by the level of resistance within each
channel that is subject to fluid viscosity and channel dimensions
(cross-section and length). In such cases, flow control is achieved
by providing channel segments with the appropriate dimensions to
achieve the desired flow rate given the viscosity of the fluids
passing through it. By way of example, in order to achieve
equivalent flow rates, channels used to flow more viscous fluids
may be provided with wider and/or shorter channel segments than
channels used to transport lower viscosity fluids.
[0091] Although described as a pressure source applied to channel
origins, in some aspects, the pressure source may include a vacuum
(or negative pressure) source that is applied to one or more of the
outlet ports for a channel network, e.g., a terminal reservoir,
i.e., reservoir 444 in FIG. 4. Application of a vacuum provides a
number of advantages over positive pressure driven systems,
including, e.g., provision of a single point of connection to an
integrated channel network at the outlet vs. several inlet points,
lack of microcapsule compression that may lead to channel inlet
clogging in positive pressure systems, and the like.
[0092] In some cases, for the partitioning of microcapsules, the
vacuum source may be applied to a node on an outlet channel segment
that is distinct from the zone at which the partitioned
microcapsules may be harvested. In particular, where a vacuum
source is applied at the terminal reservoir, e.g., reservoir 438 in
FIG. 4, the source can be disconnected from the reservoir in order
to harvest the partitioned microcapsules from the terminal
reservoir. In some cases, by separating the vacuum source interface
node with the channel segment from the zone where partitioned
microcapsules are harvested, one can obviate the need for
disconnecting the vacuum source and improving the ease of use. In
some cases, the vacuum interface node may include a terminal
reservoir, e.g., reservoir 438, which may be configured with an
interface component for interfacing with an integrated or discrete
partition harvesting zone that allows harvesting of the partitions
without removing the connected vacuum source. These and other
interface components are described in detail below.
III. Additional Improved Microfluidic System Components
[0093] The precise handling and manipulation of microcapsules,
either in their creation, or in their subsequent partitioning,
creates a number of new challenges in microfluidic systems that are
addressed by aspects of the present disclosure. In particular, flow
of microcapsule in fluidic and especially microfluidic systems can
be subject to certain variabilities many of which have been alluded
to above, including varied flow rates or dispensing frequencies,
channel clogging, variable partitioning, sampling or dispensing
biases, or the like. This disclosure provides numerous improved
components, devices, methods and systems for addressing many of
these issues.
[0094] For example, in certain aspects, the present disclosure
addresses, e.g., sampling biases or variability from microcapsules
in a reservoir. In particular, in some cases, one or more
reservoirs into which microcapsules are deposited in a system or
device described herein, e.g., reservoir 430 shown in FIG. 4, are
configured to improve the flow of microcapsules into their
connected channel segments.
[0095] In one example, the reservoirs that are used to provide the
microcapsules or other reagents may be provided with a conical
bottom surface to allow for funneling of the microcapsules toward
the inlets for the channel segments connected to the reservoirs.
This is schematically illustrated in FIG. 5A, which shows an
example of reservoirs 500, 502, 504 and 506, viewed from the side.
As shown, the reservoir 500 includes side walls 510 that extend
from an upper surface 512 of a microfluidic device 506. An interior
cavity portion 508 of the reservoir extends into the microfluidic
device 506 and is provided in communication with a fluidic channel
516. As shown, cavity portion 508 possesses a tapering or conical
shape toward the inlet of channel 516, as defined by narrowing of
the cavity 508, by virtue of converging sidewalls 518 of cavity
508.
[0096] In additional aspects, microcapsule loading into channel
segments may be enhanced through the inclusion of a broadened
interface region, or inlet, between the reservoir and the connected
fluid channel. One example of this is illustrated in the channel
network of FIG. 4, where the interface of channel segment 402 with
reservoir 430 is provided with funneling channel structure 452,
that both enhances the introduction of microcapsules into the
channel segment, as well as provides some flow regulating
characteristics for the microcapsules into the channel segment.
Also shown, are obstructive structures 454, that provide barriers
for larger particulate matter that may be a contaminant within the
reservoir and may impair the flow of fluids through the channels of
the device. As will be appreciated, the various reservoirs may each
or all include filtration or particle blocking elements within them
that mat be the same or different, depending upon the fluids to be
disposed in the reservoir. For example, in some cases, while a
simple structural barrier, like the pillar structures shown in FIG.
4 (e.g., structures 454) may be used in the channel interfaces with
the microcapsule containing reservoirs, for those reservoirs
containing aqueous solutions, e.g., sample materials or reagents,
more or less stringent filtration components may be integrated
therein, e.g., at the bottom of a reservoir, in order to filter the
contents of the reservoir, in situ, to a greater or lesser degree.
A variety of filtration media, including, e.g., membrane filters,
frits, or other known filter types, can be readily incorporated
into the reservoirs within the devices of the present
disclosure.
[0097] Similar to the broadened interfaces described above, the
interfaces may include multiple discrete channel inlets from a
given reservoir, to ensure that the flow of microcapsules into and
through the channel segments is less susceptible to interruption or
clogging, as well as to ensure that microcapsules disposed in the
reservoir are accessed at multiple points, rather than at a single
point or channel inlet. In particular, for a given reservoir, there
may be provided a plurality of channel inlets that fluidly connect
the reservoir to a single channel segment (or flow regulating
junction, as described in greater detail below) within the
microfluidic device. Further, as described above, the multiple
channel inlets may be provided with one or more of the functional
elements described previously, e.g., funneling structures,
filtering elements such as pillars, posts or tortuous paths, or the
like.
[0098] As noted in the discussion of the microcapsule partitioning
above, the flow of microcapsules, along with the flow of the other
fluids coming together in the partitioning zone, e.g., junction 322
in FIG. 3, can be controlled so as to substantially provide for a
desired number of microcapsules per partition. In many cases, the
substantial majority of occupied partitions (e.g., partitions
containing one or more microcapsules) will include no more than 1
microcapsule per occupied partition, while in some cases also
reducing the number of unoccupied partitions created.
[0099] As described above, the methods, devices and systems of the
present disclosure generally accomplish a desired level of
allocation of microcapsules to partitions through the controlled
combination of the microcapsules and partitioning or dispersion
fluid into droplets, e.g., through controlling the flow rates of
microcapsules and oil in to the droplet generating junction of a
microfluidic device, i.e., junction 312 as shown in FIG. 3.
[0100] Flowing of microcapsules from reservoirs through channels
and into channel junctions can be subject to a great deal of
variability, as these microcapsules may flow at a that is defined
by the happenstance of when the microcapsule enters a channel
segment, and its flow rate through that channel segment.
Accordingly, in certain aspects, the microfluidic systems of the
present disclosure may include microcapsule flow regulator
components within the appropriate channel segment to provide such
microcapsules flowing into the droplet forming region at a more
defined regularity.
[0101] The microcapsule flow regulators included within the channel
systems described herein will typically provide microcapsules
flowing within channels at a relatively regular frequency. In
particular, during a given timeframe in which droplets are being
generated, e.g., a 10 second window, a 30 second window, a one
minute window, a 2 minute window, a 3 minute window, or over the
steady state operation of an entire droplet generation run (e.g.,
not including start up and shut down), the frequency at which these
microcapsules are flowing will typically have a coefficient of
variation of less than 50%, less than 40%, less than 30%, less than
20%, less than 10%, and in some cases, less than 5%. As will be
appreciated, the flow frequency of microcapsules reflects the
number of microcapsules that flow past a given point in a conduit
within a one second period of time. Frequency measurements may
typically be based upon sub-second or one second intervals, but may
also be based upon multiple second, multiple minute or longer
intervals, depending upon the particular needs of the process.
[0102] Although in a given process, it may be desirable to flow
microcapsules at a relatively stable frequency, in a number of
aspects, the frequency for the flowing microcapsules can differ
depending upon the desired applications, the nature of the fluids
being flowed, and the like. In general, however, microcapsules
being flowed into a partitioning or droplet generating junction are
flowed at greater than 50 Hz, greater than 100 Hz, greater than 250
Hz, greater than 500 Hz, greater than 750 Hz, greater than 1000 Hz,
greater than 1500 Hz, greater than 2000 Hz, or even greater than
5000 Hz or even 10,000 Hz, while still achieving the desired
occupancy and other process goals. In certain cases, these flow
frequencies may be maintained after the partitioning junction, such
that partitioned microcapsules are flowing out of the droplet
generation junction at frequencies of at least or greater than 50
Hz, at least or greater than 100 Hz, at least or greater than 500
Hz, at least or greater than 750 Hz, at least or greater than 1000
Hz, at least or greater than 1500 Hz, at least or greater than 2000
Hz, or even at least or greater than 5000 Hz or 10,000 Hz.
[0103] A number of approaches may be adopted to regulate bead flows
within the microfluidic channel segments of the devices described
herein. For example, in some cases, these regulators include
"gathering zones" in which the microcapsules will flow into and
gather before flowing out of the gathering zone. These zones are
configured to more effectively meter the flow of the microcapsules
through the inclusion of funneling structures or channel profiles
to better meter the flow of individual microcapsules. Examples of
such structures are alluded to above, and are shown in FIGS. 4 and
6B. A first example includes the channel interface shown as
funneling zone 452 integrated within the interface of channel
segment 402 and reservoir 430.
[0104] In a similar fashion, a microcapsule flow regulator may be
integrated within the channel segment itself, e.g., channel segment
402 in FIG. 4, rather than at the interface with the reservoir,
e.g., reservoir 430 of FIG. 4. An example of this structure
includes the flow regulator structure 600 illustrated in FIG. 6A.
As will be appreciated, the microcapsule flow regulating structure
460 may also function as a passive fluid valve during filling of
the device, e.g., valve 436, as described with respect to channel
segments 402, 404 and 406, above. As with funneling structure 452,
flow regulator 600 includes a broadened region of channel segment
602 (shown at the interface as channel 602a) at region 604 that
narrows at region 606 until it rejoins the cross-sectional
dimensions of the outlet portion of channel segment 602 (shown at
the interface as segment 602b). As the microcapsules entered the
expanded region 602, the convective flow will allow multiple
microcapsules to gather or aggregate within the overall gathering
region. Once sufficient numbers of microcapsules have aggregated,
they will begin to flow out through the narrowed region into
channel segment 604 in a metered and more controlled manner. This
is schematically illustrated in FIG. 6B, showing microcapsules
flowing at irregular frequency into the microcapsule flow
regulating structure, and flowing out of the regulator at a more
regular frequency. As will be appreciated, a channel network may
include one or more flow regulators arranged in series or in
parallel within a given flow path, e.g., the fluid connection
between two points in the overall network. While these flow
regulators may include those having the shape and configuration as
shown in FIGS. 6 A and 6B, they may also include different shapes
and configurations. For example, the broadened regions of the flow
regulator may include triangular shapes similar to that shown in
FIGS. 6A and 6B, or may include elongated triangular shapes.
Likewise, the broadened region of the flow regulators may include
circular, elliptical or semi-circular or semi-elliptical shapes, or
may include a tapered funnel shape like the channel interfaces
described elsewhere herein. As will be appreciated, the basic
structural components of these exemplary flow regulators is a
broadened channel region at the point a flow enters into the
regulator, with a tapered, narrowing or funneling portion as the
flow enters into the subsequent channel or channel network. These
broadened regions will typically have wider cross sections that are
from 1.1.times. to 20.times. the cross section of channel segments
flowing into the broadened region. In some aspects, these broadened
regions are anywhere from 2.times. to 10.times. the cross-section
of the entering channel segment (as compared against the same
cross-sectional measurement, e.g., width to width, depth to depth,
etc.), and in some cases, from 2.times. to 5.times. the cross
section of the entering channel segment. In some cases, more than
one cross-sectional dimension may be varied over the inlet channel,
e.g., both width and depth may be different. Further, although in
some aspects, where both dimensions are varied, they will be
greater than those of the inlet channel, in some cases, provided at
least one of width and depth is increased, the other dimension may
be decreased, depending upon the desired flow characteristics
through the flow regulator.
[0105] In other examples, multiple microcapsule containing channels
are brought together at a gathering zone to bring in a higher
number of microcapsules into the junction and its connected
effluent channel segment. This allows voids in the flow of
microcapsules in one channel to be filled by microcapsules flowing
in from the other channel(s). These channel segments may include
separate channel segments provided within the channel network as a
gathering zone, or as noted above, they may comprise multiple inlet
channel segments that are fluidly connected to a microcapsule
containing reservoir. Further, as noted previously, these channel
segments may deliver microcapsules from a single source or
population of microcapsules to the same channel segment, or they
may deliver microcapsules from different sources, e.g., reservoirs,
to a common channel segment, where such different microcapsules
include different reagents.
[0106] As noted above, the microfluidic devices and systems of the
present disclosure may include improved interface components useful
in operation of the devices and systems, and interface components
that may be particularly useful in the handling and manipulation of
microcapsule compositions and partitioned compositions.
[0107] Examples of interfaces useful for microcapsule and partition
manipulation include those useful for one or both of deposition and
harvesting of such compositions to and from such devices. For
example, as noted previously, movement and transport of
microcapsules in solution can be subject to some variability. This
variability can, in some instances, carry over to transport of
these solutions from the systems in which they are created into
other systems and/or vessels, e.g., storage vessels such as tubes,
wells, vials, or the like, or in transporting them from storage
vessels, e.g., tubes, wells, vials or the like, into systems for
their subsequent processing, e.g., microfluidic partitioning
systems like those described above. In one example, a microcapsule
solution or suspension is provided within a storage vessel that
includes a pierceable wall or base surface. Corresponding piercing
structures may be provided within a reservoir on a fluidic device.
By inserting the storage vessel into the reservoir, the pierceable
wall is penetrated by the piercing structures to release the
microcapsule suspension into the reservoir.
[0108] An example of this type of interface is schematically
illustrated in FIGS. 7A and 7B. As shown in FIG. 7A, a storage
vessel, such as tube 702 is provided for holding fluid reagents,
such as a microcapsule suspension 704, as described elsewhere
herein. A surface of the vessel, e.g., base surface 706 is provided
as a pierceable layer. Pierceable layers may be provided in any of
a variety of different configurations. For example, they may simply
include walls of the same material as the rest of the vessel, but
which are sufficiently thin to allow piercing. Such walls may be
thinner than other walls in the vessel. Alternatively, the
pierceable surfaces may include different materials from that of
the remainder of the vessel, such as a pierceable septum (e.g.,
nitrocellulose, PVDF, latex, or any other similarly used
materials), a foil surface, or any of a number of other pierceable
membranes. Likewise, a surface of the storage vessel may be
provided with a valving structure that may be active or passive. In
many cases, passive valves, such as pressure triggered check valves
may be employed in base surface 706 of the storage vessel.
[0109] In use, the storage vessel is mated with the reservoir 708
in a device 710, as shown in FIG. 7B. Reservoir 708 is configured
with piercing structures 712 that are positioned to contact and
penetrate the base surface 706 of the storage vessel when the
vessel is inserted into the reservoir 708. Once inserted, the base
surface 706 is ruptured and the microcapsule suspension 704
contained in vessel 702 is permitted to drain into reservoir 708.
In some cases, vessel 702 may be provided with additional
components to facilitate driving of the suspension into the
reservoir, such as a plunger or other pressurizing device, to force
the suspension from the vessel. In other cases, simple gravity flow
may be used to transfer the suspension. In some cases, the piercing
structure and wall or base component of the vessel maybe configured
to optimize the transfer of the suspension from the vessel to the
reservoir, through the inclusion of hydrophobic interior coatings
on the vessel, flash-mitigating piercing structures (e.g., to
reduce the possibility that remnants of the pierced surface may
block flow of the suspension out of the vessel). In alternate
aspects, dissolvable, degradable or otherwise activatable barriers
may be provided in order to allow for the controlled dispensing of
the suspension. Such barriers include, e.g., dissolvable films or
membranes that are degraded, dissolved or rendered sufficiently
permeable to dispense the suspension upon application of a
stimulus. Such barriers may be degraded upon application of a
specific chemical, thermal, electromagnetic, or other stimulus.
[0110] Similar to the interfaces described above, in some cases for
harvesting either microcapsules or partitioned microcapsules or
other materials from devices, such interface components may
include, e.g., a pierceable base layer for the harvesting
reservoir, e.g., reservoir 216 shown in FIG. 2, or reservoir 438 of
the device illustrated in FIG. 4, to allow access to and removal of
partitioned microcapsules from the terminal reservoir without
necessarily removing the interfaced vacuum source. In operation, at
the conclusion of a partitioning operation, the base of the
terminal reservoir may be pierced, and the generated partitions are
either removed or allowed to drain or flow into a waiting
receptacle, e.g., by reversing the vacuum source to apply pressure
to the reservoir 438, to drive the partitioned microcapsules
through the pierced base layer of the reservoir, or through gravity
driven flow. This waiting receptacle may be integrated into the
device, or positioned adjacent to the microfluidic device in order
to receive the partitioned microcapsules.
[0111] In other examples, one or both of the reservoir and storage
vessel may be configured to provide efficient transfer from one to
the other. For example, in some cases, a vessel including a
microcapsule suspension may be provided with an interface component
that allows it to be mated, connected and/or coupled directly to
the receiving reservoir to efficiently transfer its contents. In
some cases, the connection may be bounded by a check valve to
prevent movement of the suspension until an appropriate driving
force is applied to the suspension.
[0112] In addition to fluidic interfaces, the devices and systems
described herein may also include one or more of a variety of
mechanical or physical interface components. Such components
include, for example, handling components to facilitate the manual
or automated movement and handling of the devices, alignment
components, to ensure proper placement and alignment of the devices
on instruments, holders and the like, as well as functional
components, to allow for additional manipulation of sample
materials within the devices. Examples of handling components
include tabs, walls, or other surfaces that are positioned away
from critical or sensitive surfaces of a device (e.g., optical
windows, surfaces prone to contamination, etc.), as well as
surfaces that are configured to facilitate handling, whether manual
or automated, e.g., with sufficient size and/or textured surfaces
to ensure grip and control.
[0113] Examples of alignment structures include mechanical elements
that ensure alignment of a device with a corresponding instrument,
or other fixture, such as beveled corners, device shapes, and
integrated key elements (e.g., tabs, slots, posts, or the like)
that mate with complementary structures on the other fixture. Such
alignment components also include optically detected components,
such as registration marks or fiducials, barcode tags, or other
machine readable components integrated into or attached to a
device.
[0114] A wide variety of functional components or functional
component interfaces are also envisioned, including, e.g., those
interface components that are important for operation of the
device. Examples of such interface components include, for example,
gasket structures that may be integrated into or separately placed
over the upper surfaces of one or more reservoirs, to ensure sealed
application of pressures or vacuums to the devices described
herein. In certain aspects, these gaskets will be either integrated
into the device, or provided as a separate, disposable component,
rather than being integrated into an instrument, in order to
minimize the possibility of instrument contamination. Other
examples of functional interface components include interfaces for
mixing or agitating components within the reservoirs. Such
components are useful in come cases to prevent settling of
microcapsule compositions. These interfaces may comprise actual
agitation components, such as piezoelectric, acoustic, or
mechanical vibration components integrated into the devices, or
they may comprise surfaces that are suitable for or are configured
to interface these components on a corresponding instrument system
or other fixture.
[0115] While the foregoing invention has been described in some
detail for purposes of clarity and understanding, it will be clear
to one skilled in the art from a reading of this disclosure that
various changes in form and detail can be made without departing
from the true scope of the invention. For example, all the
techniques and apparatus described above can be used in various
combinations. For example, particle delivery can be practiced with
array well sizing methods as described. All publications, patents,
patent applications, and/or other documents cited in this
application are incorporated by reference in their entirety for all
purposes to the same extent as if each individual publication,
patent, patent application, and/or other document were individually
and separately indicated to be incorporated by reference for all
purposes.
* * * * *