US Pat. No. 9,388,465

POLYNUCLEOTIDE BARCODE GENERATION

10X GENOMICS, INC., Plea...

1. A method of synthesizing a library of polynucleotides comprising barcode sequences, said method comprising:
synthesizing a plurality of polynucleotides comprising barcode sequences;
separating said polynucleotides into a plurality of partitions, thereby generating partitioned polynucleotides, wherein each
partition comprising a polynucleotide comprises multiple copies of the same polynucleotide comprising a barcode sequence prior
to amplifying said partitioned polynucleotides;

amplifying said partitioned polynucleotides, thereby generating a library of amplified polynucleotides, comprising at least
about 100,000 different barcode sequences;

wherein said amplified polynucleotides are attached to a bead; and
isolating partitions comprising amplified polynucleotides.
US Pat. No. 9,410,149

COMPOSITIONS AND METHODS FOR INTRAMOLECULAR NUCLEIC ACID REARRANGEMENT

10X Genomics, Inc., Plea...

1. A method of analyzing genomic DNA, comprising:
a) generating a first plurality of different segments of a first nucleic acid molecule of a contiguous region in the genomic
DNA, wherein said contiguous region in the genomic DNA is represented by a plurality of nucleic acid molecules, and wherein
each of said first plurality of different segments is appended to a first multiplex identifier (MID) sequence;

b) generating a second plurality of different segments of a second nucleic acid molecule of said contiguous region, wherein
each of said second plurality of different segments is appended to a second MID sequence and said first MID sequence and said
second MID sequence are different; and

c) sequencing the first and second plurality of different segments and the appended first and second MID sequences, respectively,
to analyze the genomic DNA.

US Pat. No. 9,410,150

COMPOSITIONS AND METHODS FOR INTRAMOLECULAR NUCLEIC ACID REARRANGEMENT

10X Genomics, Inc., Plea...

1. A composition comprising:
a) a first plurality of different segments of DNA from a first sample, wherein the first plurality of different segments of
DNA are derived from a first nucleic acid molecule of a locus in genomic DNA and wherein each of said first plurality of different
segments is appended to a first sequence tag; and

b) a second plurality of different segments of DNA from the first sample, wherein the second plurality of different segments
of DNA are derived from a second nucleic acid molecule of the locus and wherein each of said second plurality of different
segments is appended to a second sequence tag and said first sequence tag and said second sequence tag are different.

US Pat. No. 9,410,201

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method of nucleic acid sequence analysis, comprising:
(a) fragmenting a first nucleic acid molecule to provide a plurality of polynucleotide molecules;
(b) partitioning the plurality of polynucleotide molecules of the first nucleic acid molecule into a plurality of separate
partitions, wherein each of the plurality of separate partitions comprises:

i. at least 20 polynucleotide molecules from the plurality of polynucleotide molecules, the at least 20 polynucleotide molecules
comprising non-overlapping fragment polynucleotide molecules; and

ii. a plurality of barcode molecules, wherein each barcode molecule within a given partition shares a common barcode sequence
and is associated with a bead within the partition;

(c) after (b), generating barcoded fragment molecules from the at least 20 polynucleotide molecules and plurality of barcode
molecules within each of the separate partitions; and

(d) analyzing the barcoded fragment molecules generated in (c), thereby analyzing a nucleic acid sequence of the first nucleic
acid molecule.

US Pat. No. 9,824,068

METHODS AND APPARATUS FOR SORTING DATA

10X Genomics, Inc., Plea...

1. A method for data processing, comprising:
(a) obtaining a particular string data value from among a plurality of string data values, wherein each of the plurality of
string data values comprises a portion of a genome sequence, and wherein the plurality of string data values is obtained from
a genome sequence machine;

(b) mapping with a programmed computer processor the particular string data value to a particular data container among a plurality
of data containers, wherein each of the plurality of string data values is addressable by a position in the genome sequence
such that the plurality of data containers is ordered with respect to the genome sequence;

(c) appending a data item comprising the particular string data value to the particular data container in a computer memory;
(d) repeating (b)-(c) with the programmed computer processor for all of the plurality of string data values; and
(e) outputting a continuous output sequence generated from (a)-(d), wherein (a)-(d) are performed in the absence of sorting
the plurality of string data values.

US Pat. No. 9,644,204

PARTITIONING AND PROCESSING OF ANALYTES AND OTHER SPECIES

10X GENOMICS, INC., Plea...

1. A composition comprising a plurality of capsules, said capsules situated within droplets in an emulsion, wherein said capsules
are configured to release their contents into said droplets upon the application of a stimulus to provide said contents in
said droplets in said emulsion, wherein said stimulus is selected from the group consisting of a change in pH, a change in
ion concentration, reduction of disulfide bonds, and combinations thereof.
US Pat. No. 10,053,723

CAPSULE ARRAY DEVICES AND METHODS OF USE

10X GENOMICS, INC., Plea...

1. A composition for use in barcoding nucleic acid molecules, comprising:a population of at least 1,000 gel beads comprising a plurality of nucleic acid barcode molecules,
wherein a given gel bead of said at least 1,000 gel beads comprises at least 1,000 nucleic acid barcode molecules of said plurality of nucleic acid barcode molecules,
wherein at least (i) a first subset of said at least 1,000 nucleic acid barcode molecules is coupled to an interior surface of said given gel bead, and (ii) a second subset of said at least 1,000nucleic acid barcode molecules is coupled to an outer surface of said given gel bead, and
wherein each of said at least 1,000 nucleic acid barcode molecules comprises an identical barcode sequence that differs from barcode sequences of barcode molecules comprised in other gel beads of said at least 1,000 gel beads.
US Pat. No. 9,982,297

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for analyte characterization, comprising:(a) providing a plurality of partitions, wherein a partition of said plurality of partitions comprises a plurality of barcode molecules and a plurality of analytes, wherein said plurality of barcode molecules is coupled to a bead, wherein (i) a first individual barcode molecule of said plurality of barcode molecules comprises a first nucleic acid barcode sequence and is capable of coupling to a first analyte of said plurality of analytes, and (ii) a second individual barcode molecule of said plurality of barcode molecules comprises a second nucleic acid barcode sequence and is capable of coupling to a second analyte of said plurality of analytes, wherein said first analyte and said second analyte are different types of analytes; and
(b) in said partition,
(i) using at least a portion of said first individual barcode molecule and said first analyte to synthesize a first nucleic acid molecule comprising (1) at least a portion of said first nucleic acid barcode sequence or a complement of said portion of said first nucleic acid barcode sequence and (2) a first sequence of said first analyte or a complement of said first sequence; and
(ii) using at least a portion of said second individual barcode molecule and said second analyte to synthesize a second nucleic acid molecule comprising (1) at least a portion of said second nucleic acid barcode sequence or a complement of said portion of said second nucleic acid barcode sequence and (2) a second sequence of said second analyte or a complement of said second sequence; and
(c) removing or releasing said first nucleic acid molecule and said second nucleic acid molecule from said partition,
wherein, after (a), said first individual barcode molecule or said second individual barcode molecule is released from said bead.
US Pat. No. 9,856,530

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for nucleic acid preparation or analysis, comprising:
(a) providing:
(i) at least 1,000 gel beads;
(ii) releasably attached to each of said at least 1,000 gel beads, at least 1,000 barcode molecules comprising identical barcode
sequences that are distinct from barcode sequences of at least 1,000 barcode molecules releasably attached to any other gel
bead of said at least 1,000 gel beads; and

(iii) a plurality of cells each comprising a plurality of polynucleotide molecules;
(b) generating a plurality of droplets, wherein at least 1,000 droplets of said plurality of droplets each comprise:
(i) a single gel bead from said at least 1,000 gel beads; and
(ii) a single cell from said plurality of cells; and
(c) in each of said at least 1,000 droplets, using said plurality of polynucleotide molecules from said single cell and barcode
molecules of said at least 1,000 barcode molecules from said single gel bead to generate a plurality of barcoded polynucleotide
molecules,

wherein said barcode molecules become detached from said gel bead.
US Pat. No. 9,695,468

METHODS FOR DROPLET-BASED SAMPLE PREPARATION

10X GENOMICS, INC., Plea...

1. A method for droplet generation, comprising:
(a) providing at least 1,000,000 oligonucleotide molecules comprising barcode sequences, wherein said barcode sequences are
the same sequence for said at least 1,000,000 oligonucleotide molecules, wherein said at least 1,000,000 oligonucleotide molecules
are releasably attached to a bead, wherein said bead is porous;

(b) combining said at least 1,000,000 oligonucleotide molecules and a sample comprising a nucleic acid analyte each in an
aqueous phase at a first junction of two or more channels of a microfluidic device to form an aqueous mixture comprising said
at least 1,000,000 oligonucleotide molecules attached to said bead and said sample; and

(c) generating a droplet comprising said at least 1,000,000oligonucleotide molecules attached to said bead and said sample
comprising said nucleic acid analyte by contacting said aqueous mixture with an immiscible continuous phase at a second junction
of two or more channels of said microfluidic device.

US Pat. No. 9,689,024

METHODS FOR DROPLET-BASED SAMPLE PREPARATION

10X GENOMICS, INC., Plea...

1. A method for sample preparation, comprising:
a) providing a droplet comprising a porous gel bead and a target nucleic acid analyte, wherein said porous gel bead comprises
at least 1,000,000 oligonucleotide molecules comprising barcode sequences, wherein said oligonucleotide molecules are releasably
attached to said porous gel bead, wherein said barcode sequences are the same sequence for said oligonucleotide molecules;

b) applying a stimulus to said porous gel bead to release said oligonucleotide molecules from said porous gel bead into said
droplet, wherein upon release from said porous gel bead, a given oligonucleotide molecule from said oligonucleotide molecules
attaches to said target nucleic acid analyte; and

c) subjecting said given oligonucleotide molecule attached to said target nucleic acid analyte to nucleic acid amplification
to yield a barcoded target nucleic acid analyte.

US Pat. No. 9,701,998

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X Genomics, Inc., Plea...

1. A method of nucleic acid sequence analysis, comprising:
(a) providing a plurality of partitions comprising a plurality of polynucleotide molecules and a plurality of barcode molecules,
wherein:

i. said plurality of partitions comprises at least 1,000 partitions;
ii. said plurality of barcode molecules comprises at least 1,000 different nucleic acid barcode molecules having different
barcode sequences;

iii. said at least 1,000 different nucleic acid barcode molecules are disposed within separate partitions of said at least
1,000 partitions, such that each of said at least 1,000 partitions has a different barcode sequence of said different barcode
sequences; and

iv. said at least 1,000 partitions are at least 1% of said plurality of partitions;
(b) subsequent to (a), generating a plurality of barcoded molecules from said plurality of polynucleotide molecules and said
plurality of barcode molecules within said plurality of partitions; and

(c) directing said plurality of barcoded molecules generated in (b) to nucleic acid sequencing, wherein a sequence of a given
polynucleotide of said plurality of polynucleotide molecules is determined.

US Pat. No. 9,694,361

FLUIDIC DEVICES, SYSTEMS, AND METHODS FOR ENCAPSULATING AND PARTITIONING REAGENTS, AND APPLICATIONS OF SAME

10X Genomics, Inc., Plea...

1. A method for partitioning microcapsules, comprising:
(a) providing a microfluidic device comprising a microfluidic channel network, wherein the microfluidic channel network comprises
(i) a droplet generation junction, (ii) a first channel segment fluidly connecting a source of microcapsules to the droplet
generation junction, (iii) a second channel segment fluidly connecting a source of partitioning fluid to the droplet generation
junction, and (iv) a third channel segment fluidly connected to the droplet generation junction and providing an outlet to
the droplet generation junction; and

(b) flowing (i) an aqueous fluid comprising a suspension of microcapsules from the source of microcapsules along the first
channel segment and (ii) a partitioning fluid from the source of partitioning fluid along the second channel segment into
the droplet generation junction to form a population of droplets of the aqueous fluid in the partitioning fluid, wherein the
population of droplets flow along the third channel segment, and wherein (1) the first channel segment has a cross-sectional
dimension that provides a flow rate of the aqueous fluid or (2) the second channel segment has a cross-sectional dimension
that provides a flow rate of the partitioning fluid, such that greater than 50% of droplets of the population of droplets
are occupied by microcapsules from the suspension of microcapsules.

US Pat. No. 9,567,631

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method comprising:
(a) providing a target polynucleotide;
(b) fragmenting said target polynucleotide to generate a plurality of non-overlapping first polynucleotide fragments;
(c) partitioning said first polynucleotide fragments to generate partitioned first polynucleotide fragments, wherein at least
one partition of said partitioned first polynucleotide fragments comprises a first polynucleotide fragment with a unique sequence
within said at least one partition; and

(d) fragmenting said partitioned first polynucleotide fragments to generate a plurality of second polynucleotide fragments,
wherein in (b)-(c), the plurality of non-overlapping first polynucleotide fragments is not quantified.
US Pat. No. 10,071,377

FLUIDIC DEVICES, SYSTEMS, AND METHODS FOR ENCAPSULATING AND PARTITIONING REAGENTS, AND APPLICATIONS OF SAME

10X GENOMICS, INC., Plea...

1. 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 microcapsules;
a second fluid source fluidly connected to a second channel and comprising a second fluid that is immiscible with the aqueous fluid;
a droplet generation junction fluidly connected to a third channel;
a flow regulator fluidly connected to the first channel and a fourth channel, wherein the flow regulator (1) accepts microcapsules from the plurality of microcapsules from the first channel and (2) provides the microcapsules in the fourth channel, wherein the flow regulator has a cross-section that is greater than a cross-section of the first channel such that the microcapsules flow at a flow frequency that is substantially regular in the fourth channel as determined by a number of microcapsules that flow past a given point in the fourth channel within a one second period of time;
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 fourth channel, such that the microcapsules from the plurality of microcapsules flow at the flow frequency that is substantially regular in the fourth channel as determined by the number of microcapsules that flow past the given point in the fourth channel within the one second period of time, and
(ii) subjects the second fluid from the second fluid source to flow along the second channel, such that the microcapsules and the second fluid meet at the droplet generation junction to generate a plurality of droplets comprising the microcapsules from the plurality of microcapsules, which plurality of droplets flow along the third channel.
US Pat. No. 10,041,116

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for identifying an analyte from a single cell, comprising:(a) causing an analyte of said single cell to contact one or more antibodies, thereby providing an antibody from said one or more antibodies coupled to said analyte, wherein said antibody is associated with a first nucleic acid molecule comprising a first barcode sequence;
(b) using said first nucleic acid molecule and a second nucleic acid molecule to generate a third nucleic acid molecule, wherein said second nucleic acid molecule comprises a second barcode sequence, and wherein said third nucleic acid molecule comprises (i) said first barcode sequence or a complement thereof, and (ii) said second barcode sequence or a complement thereof;
(c) processing said third nucleic acid molecule or a derivative thereof to identify said first barcode sequence and said second barcode sequence; and
(d) using said first barcode sequence and said second barcode sequence identified in (c) to identify said analyte of said single cell.

US Pat. No. 9,946,577

SYSTEMS AND METHODS FOR DISTRIBUTED RESOURCE MANAGEMENT

10X GENOMICS, INC., Plea...

1. A computing system comprising one or more processors and a memory, the memory storing one or more programs for execution by the one or more processors, the one or more programs singularly or collectively comprising instructions for executing a method comprising:for a first epic in a plurality of epics:
(A) identifying a first plurality of jobs in a queue, wherein each respective job in the first plurality of jobs is associated with a timestamp that indicates when the respective job was submitted to the queue and specifies one or more node resource requirements;
(B) determining a composite computer memory requirement and a composite processing core requirement, for the first plurality of jobs, from the one or more node resource requirements of each job in the first plurality of jobs;
(C) identifying a first plurality of nodes to add to a cluster during the first epic to satisfy at least a subset of the composite computer memory requirement and the composite processing core requirement, wherein the identifying (C) comprises:
(i) obtaining, for each respective node class in a first plurality of node classes: (a) a current availability score, (b) a reservable number of processing cores, and (c) a reservable memory capability of the respective node class, and
(ii) submitting a request for one or more nodes of a corresponding node class in the first plurality of node classes when a demand score for the corresponding node class satisfies the current availability score for the corresponding node class by a first threshold amount, thereby identifying the first plurality of nodes to add to the cluster of nodes during the first epic;
(D) adding the first plurality of nodes to the cluster of nodes during the first epic; and
(E) granting each respective node in the cluster of nodes with a draw privilege, wherein the draw privilege permits a respective node to draw one or more jobs from the queue during the first epic subject to a constraint that the collective computer memory requirements and processing core requirements of the one or more jobs collectively drawn by a respective node in the cluster of nodes does not exceed a number of reservable processing cores and a reservable memory capability of the respective node, and wherein a first node in the cluster of nodes draws more than one job from the queue for concurrent execution on the first node during the first epic.
US Pat. No. 9,951,386

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for single cell processing or analysis, comprising:(a) causing a single cell from a plurality of cells to contact one or more antibodies such that an antibody from said one or more antibodies couples to said single cell, wherein said antibody is associated with a first nucleic acid molecule comprising a first barcode sequence;
(b) co-partitioning said single cell having said antibody coupled thereto with a single bead from a plurality of beads in a droplet, wherein said single bead comprises a second nucleic acid molecule comprising a second barcode sequence; and
(c) generating from said first nucleic acid molecule and said second nucleic acid molecule, a third nucleic acid molecule comprising (i) said first barcode sequence or a complement thereof, and (ii) said second barcode sequence or a complement thereof.
US Pat. No. 10,030,267

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for identifying a protein as originating from a single cell, comprising:(a) exposing said protein of said single cell to one or more antibodies such that an antibody of said one or more antibodies that is specific to said protein couples to said protein, wherein said antibody is conjugated to a nucleic acid antibody barcode molecule comprising an antibody barcode sequence;
(b) co-partitioning said single cell comprising said protein coupled to said antibody with a single bead in a partition, wherein said single bead comprises a plurality of nucleic acid cell barcode molecules each comprising a cell barcode sequence;
(c) performing one or more reactions to generate, from said nucleic acid antibody barcode molecule and a nucleic acid cell barcode molecule from said plurality of nucleic acid cell barcode molecules, a synthesized nucleic acid molecule comprising (i) said antibody barcode sequence or a complement thereof, and (ii) said cell barcode sequence or a complement thereof;
(d) using a sequencer to sequence at least a portion of said synthesized nucleic acid molecule or a derivative thereof, to identify said antibody barcode sequence and said cell barcode sequence, and
(e) using said antibody barcode sequence and said cell barcode sequence to identify said protein as originating from said single cell.
US Pat. No. 10,011,872

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for analyte characterization, comprising:(a) providing a plurality of partitions, wherein a partition of said plurality of partitions comprises a plurality of barcode molecules and a plurality of analytes, wherein said plurality of barcode molecules is coupled to a bead, wherein (i) a first individual barcode molecule of said plurality of barcode molecules comprises a first nucleic acid barcode sequence and is capable of coupling to a first analyte of said plurality of analytes, and (ii) a second individual barcode molecule of said plurality of barcode molecules comprises a second nucleic acid barcode sequence and is capable of coupling to a second analyte of said plurality of analytes, wherein said first analyte and said second analyte are different types of analytes; and
(b) in said partition,
(i) using at least a portion of said first individual barcode molecule and said first analyte to synthesize a first nucleic acid molecule comprising (1) at least a portion of said first nucleic acid barcode sequence or a complement of said portion of said first nucleic acid barcode sequence and (2) a first sequence of said first analyte or a complement of said first sequence; and
(ii) using at least a portion of said second individual barcode molecule and said second analyte to synthesize a second nucleic acid molecule comprising (1) at least a portion of said second nucleic acid barcode sequence or a complement of said portion of said second nucleic acid barcode sequence and (2) a second sequence of said second analyte or a complement of said second sequence; and
(c) removing or releasing said first nucleic acid molecule and said second nucleic acid molecule from said partition,
wherein, after (a), said first individual barcode molecule or said second individual barcode molecule is released from said bead.

US Pat. No. 9,975,122

INSTRUMENT SYSTEMS FOR INTEGRATED SAMPLE PROCESSING

10X GENOMICS, INC., Plea...

1. An integrated system for processing samples comprised of various fluids for analysis, the system comprising:(a) a microfluidic device including a plurality of channel networks for partitioning the samples into partitioned samples, the plurality of channel networks being connected to a plurality of inlet and outlet reservoirs;
(b) a holder including a closeable lid hingedly coupled thereto,
wherein in a closed configuration, the closeable lid secures the microfluidic device in the holder, and
wherein in an open configuration, the closeable lid comprises a stand orienting the microfluidic device at an angle to facilitate recovery of the partitioned samples; and
(c) an instrument configured to receive the holder and apply a pressure differential between the plurality of inlet and outlet reservoirs to drive fluid movement within the plurality of channel networks.
US Pat. No. 10,150,964

PARTITIONING AND PROCESSING OF ANALYTES AND OTHER SPECIES

10X GENOMICS, INC., Plea...

1. A method for processing a nucleic acid sample, comprising:(a) providing a plurality of partitions, wherein a given partition of the plurality of partitions comprises the nucleic acid sample, a plurality of barcode molecules coupled to a bead, and a transposase;
(b) using the transposase to fragment the nucleic acid sample to a plurality of nucleic acid molecules in the given partition; and
(c) using barcode molecules from the plurality of barcode molecules to barcode nucleic acid molecules from the plurality of nucleic acid molecules, thereby providing barcoded nucleic acid molecules,
wherein subsequent to (a), the barcode molecules are released from the bead into the given partition.
US Pat. No. 10,150,117

FLUIDIC DEVICES, SYSTEMS, AND METHODS FOR ENCAPSULATING AND PARTITIONING REAGENTS, AND APPLICATIONS OF SAME

10X GENOMICS, INC., Plea...

1. A device for generating a droplet comprising a single microcapsule of a plurality of microcapsules, said device comprising a layered structure 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 microcapsules, wherein said microcapsules of said first fluid flow at an irregular frequency in said first channel;
(ii) a second channel connected to a droplet generation junction, wherein said second channel is configured to receive a second fluid that is immiscible with said first fluid;
(iii) a third channel connected to a droplet generation junction; and
(iv) a fourth channel connected to a second end of the flow regulator and to the 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 microcapsules of said plurality of microcapsules from said first channel to gather in said broadened channel region, and (b) allow said microcapsules gathered in said broadened channel region to flow through said funneling channel region and into said fourth channel at a regular flow frequency,
wherein said fourth channel is configured to bring said microcapsules in contact with said second fluid from said second channel at said droplet generation junction to generate a droplet comprising said single microcapsule from said microcapsules of said plurality of microcapsules, and
wherein said third channel is configured to provide an outlet for said droplet comprising said single microcapsule away from said droplet generation junction.
US Pat. No. 10,273,541

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for processing messenger ribonucleic acid (mRNA) molecules from a single cell, comprising:(a) partitioning a plurality of cells and a plurality of beads in a microwell array comprising a plurality of wells, wherein a well of said plurality of wells comprises said single cell from said plurality of cells and a single bead from said plurality of beads, and wherein said single bead comprises nucleic acid barcode molecules each comprising a common barcode sequence;
(b) in said well comprising said single cell and said single bead, releasing messenger ribonucleic acid (mRNA) molecules from said single cell, wherein upon release from said single cell, said released mRNA molecules attach to said nucleic acid barcode molecules;
(c) subjecting said released mRNA molecules attached to said nucleic acid barcode molecules to reverse transcription to yield complementary deoxyribonucleic acid (cDNA) molecules each comprising said common barcode sequence or a complement thereof; and
(d) subjecting said cDNA molecules to one or more reactions to generate a set of nucleic acid molecules for nucleic acid sequencing.
US Pat. No. 10,253,364

METHOD AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for generating a sequencing set, comprising:(a) bringing an aqueous fluid comprising a plurality of cells and a plurality of beads in contact with a continuous phase comprising an oil that is immiscible with said aqueous fluid, to generate a plurality droplets, wherein a droplet of said plurality of droplets comprises a single cell from said plurality of cells and a single bead from said plurality of beads, wherein said single bead comprises a plurality of nucleic acid barcode molecules, and wherein nucleic acid barcode molecules of said plurality of nucleic acid barcode molecules comprise a common barcode sequence;
(b) in said droplet, subjecting messenger ribonucleic acid (mRNA) molecules from said single cell to reverse transcription in the presence of said nucleic acid barcode molecules to yield barcoded complementary deoxyribonucleic acid (cDNA) molecules comprising said common barcode sequence, or a complement thereof;
(c) breaking or disputing said plurality of droplets, thereby releasing a plurality of cDNA molecules from said plurality of droplets, wherein said plurality of cDNA molecules comprises said barcoded cDNA molecules or derivatives thereof; and
(d) subjecting said plurality of cDNA molecules or derivatives thereof to one or more reactions to generate said sequencing set,
wherein, after (a), said nucleic acid barcode molecules of said plurality of nucleic acid barcode molecules are released from said single bead.
US Pat. No. 10,208,343

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A library of partitions for barcoding nucleic acid molecules, comprising:a plurality of partitions comprising a plurality of gel beads that are degradable upon application of a stimulus, wherein said plurality of gel beads comprises a plurality of barcode sequences that are different across said plurality of gel beads,
wherein a given partition of said plurality of partitions comprises a given gel bead of said plurality of gel beads and an agent configured to degrade said given gel bead,
wherein said given gel bead of said plurality of gel beads comprises a plurality of nucleic acid molecules, and
wherein each of said plurality of nucleic acid molecules comprises a barcode sequence from said plurality of barcode sequences and a unique molecular sequence, wherein (i) said barcode sequence is constant across said plurality of nucleic acid molecules, and (ii) said unique molecular sequence varies across said plurality of nucleic acid molecules.
US Pat. No. 10,150,963

PARTITIONING AND PROCESSING OF ANALYTES AND OTHER SPECIES

10X GENOMICS, INC., Plea...

1. A method for processing a nucleic acid sample, comprising:(a) providing a plurality of partitions, wherein a given partition of the plurality of partitions comprises the nucleic acid sample, a plurality of barcode molecules coupled to a bead, and a transposase;
(b) using the transposase to fragment the nucleic acid sample to a plurality of nucleic acid molecules in the given partition; and
(c) using barcode molecules from the plurality of barcode molecules to barcode nucleic acid molecules from the plurality of nucleic acid molecules, thereby providing barcoded nucleic acid molecules,
wherein subsequent to (a), the bead is subjected to conditions sufficient to disrupt the bead in the given partition.
US Pat. No. 10,233,492

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for analyzing cells comprising:(a) contacting a plurality of cells with an antibody to provide a cell bound to said antibody, wherein said antibody is attached to a reporter oligonucleotide;
(b) co-partitioning at least a subset of said plurality of cells into a plurality of wells, wherein a well of said plurality of wells comprises (i) said cell bound to said antibody and (ii) a first nucleic acid molecule comprising a barcode sequence; and
(c) using said reporter oligonucleotide and said first nucleic acid molecule to generate a second nucleic acid molecule comprising (i) a reporter sequence corresponding to a sequence of said reporter oligonucleotide and (ii) said barcode sequence.
US Pat. No. 10,227,648

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A system for nucleic acid processing, comprising:a microwell array comprising 1,000 microwells configured to partition a plurality of polynucleotide molecules, a plurality of beads, and a plurality of barcode molecules in the 1,000 microwells of the microwell array,
wherein the plurality of barcode molecules comprises a plurality of barcode sequences that are different across the 1,000 microwells, and
wherein a microwell of the microwell array comprises: (i) a polynucleotide molecule from the plurality of polynucleotide molecules; and (ii) a barcode molecule from the plurality of barcode molecules, wherein the barcode molecule is attached to a bead from the plurality of beads and comprises a barcode sequence from the plurality of barcode sequences.
US Pat. No. 10,137,449

FLUIDIC DEVICES, SYSTEMS, AND METHODS FOR ENCAPSULATING AND PARTITIONING REAGENTS, AND APPLICATIONS OF SAME

10X GENOMICS, INC., Plea...

1. A method for manufacturing a droplet generator, comprising:(a) injection molding a polymeric structure 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 a plurality of microcapsules;
(ii) a second channel connected to a droplet generation junction, wherein said second channel is configured to receive a second fluid that is immiscible with said first fluid;
(iii) a third channel connected to the droplet generation junction; and
(iv) a fourth channel connected to a second end of the flow regulator and to the droplet generation junction,
wherein a cross-section of said flow regulator (i) increases along a direction of flow from said first channel and decreases along a direction of flow to said fourth channel and (ii) is dimensioned to accept microcapsules of said plurality of microcapsules from said first channel and provide said microcapsules in said fourth channel;
wherein said fourth channel is configured to allow contact of a fluid comprising said microcapsules of said plurality of microcapsules with said second fluid from said second channel at said droplet generation junction to generate a droplet comprising a single microcapsule from said microcapsules of said plurality of microcapsules, and
wherein said third channel is configured to provide an outlet for said droplet from said droplet generation junction; and
(b) attaching a laminating structure to said polymeric structure, wherein said laminating structure seals said first channel, said second channel, said third channel, and said fourth channel.
US Pat. No. 10,287,623

METHODS AND COMPOSITIONS FOR TARGETED NUCLEIC ACID SEQUENCING

10X GENOMICS, INC., Plea...

1. A method of obtaining sequence information from one or more targeted portions of a genomic sample, the method comprising:(a) providing a plurality of fragments from the genomic sample in discrete partitions, wherein each of the fragments further comprises a barcode, and wherein at least first and second fragments within 10 kb of each other in a contiguous sequence of the genomic sample comprise a common barcode, and wherein the discrete partitions are flowable within fluid streams;
(b) applying a library of probes directed to the one or more targeted portions of the genomic sample to the plurality of fragments;
(c) conducting a first sequencing reaction to identify sequences of the plurality of fragments that hybridized to the library of probes, thereby obtaining sequence information from the one or more targeted portions of the genomic sample;
(d) conducting a second sequencing reaction to identify sequences of fragments from the discrete partitions that did not hybridize to the library of probes.

US Pat. No. 10,245,587

INSTRUMENT SYSTEMS FOR INTEGRATED SAMPLE PROCESSING

10X GENOMICS, INC., Plea...

1. A system for processing samples, comprising:a microfluidic device including a plurality of channel networks configured to partition said samples into partitioned samples, wherein a channel network of said plurality of channel networks is connected to an inlet reservoir and an outlet reservoir;
an instrument configured to interface with said microfluidic device and apply a pressure differential between said inlet reservoir and said outlet reservoir to subject fluid within said channel network to movement; and
a holder configured to receive said microfluidic device; and
a rotatable body coupled to said holder, wherein said rotatable body is configured to rotate from a closed configuration to an open configuration, or vice versa,
wherein said holder is configured to (i) secure said microfluidic device and permit said instrument to interface with said microfluidic device to apply said pressure differential when said rotatable body is in said closed configuration, and (ii) permit said microfluidic device to be inserted into or removed from said holder when said rotatable body is in said open configuration.
US Pat. No. 10,240,197

METHODS FOR ANALYZING NUCLEIC ACIDS FROM SINGLE CELLS

10X GENOMICS, INC., Plea...

1. A method of counting nucleic acids in a sample, the method comprising:(a) providing a sample comprising a plurality of cells, wherein a cell of the plurality of cells comprises a plurality of sample polynucleotides;
(b) generating a plurality of tagged polynucleotides from the plurality of sample polynucleotides of said cell and a plurality of oligonucleotide tags, wherein a tagged polynucleotide of the plurality of tagged polynucleotides comprises:
(i) a sample sequence from a sample polynucleotide of the plurality of sample polynucleotides;
(ii) a first tag sequence distinguishing said sample polynucleotide from sample polynucleotides from other cells; and
(iii) a second tag sequence distinguishing said sample polynucleotide from other sample polynucleotides from said cell;
(c) sequencing the tagged polynucleotide to determine the sample sequence, the first tag sequence, and the second tag sequence; and
(d) using the first tag sequence and the second tag sequence to count a number of sample polynucleotides in said plurality of sample polynucleotides of said cell.

US Pat. No. 10,162,678

SYSTEMS AND METHODS FOR DISTRIBUTED RESOURCE MANAGEMENT

10X GENOMICS, INC., Plea...

1. A computing system comprising one or more processors and a memory, the memory storing one or more programs for execution by the one or more processors, the one or more programs singularly or collectively comprising instructions for executing a method comprising:for a plurality of jobs in a queue, wherein each respective job in the plurality of jobs is associated with a timestamp that indicates when the respective job was submitted to the queue and specifies one or more node resource requirements:
(A) determining a composite computer memory requirement and a composite processing core requirement, for the plurality of jobs, from the one or more node resource requirements of each job in the plurality of jobs;
(B) identifying a one or more nodes to add to a cluster to satisfy at least a subset of the composite computer memory requirement and the composite processing core requirement, wherein the identifying (B) comprises:
(i) obtaining a current availability score or list price for each respective node class in a plurality of node classes, and
(ii) submitting a request for one or more nodes of a corresponding node class in the plurality of node classes when a demand score for the corresponding node class (a) satisfies the current availability score for the corresponding node class by a first threshold amount or (b) satisfies the list price for the corresponding node class;
(C) adding the one or more nodes to the cluster of nodes, wherein the adding comprises installing a distributed computing module on each respective node in the one or more nodes; and
(D) granting each respective node in the one or more nodes with a draw privilege, wherein the draw privilege permits the distributed computing module of a respective node to draw one or more jobs from the plurality of jobs subject to a constraint that the collective computer memory requirements and processing core requirements of the one or more jobs collectively drawn by a respective node in the cluster of nodes does not exceed a number of reservable processing cores and a reservable memory capability of the respective node, and wherein the respective node identifies the one or more jobs by scanning the plurality of jobs in accordance with the draw privilege.

US Pat. No. 10,343,166

FLUIDIC DEVICES, SYSTEMS, AND METHODS FOR ENCAPSULATING AND PARTITIONING REAGENTS, AND APPLICATIONS OF SAME

10X GENOMICS, INC., Plea...

1. A method for partitioning microcapsules, 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 microcapsules;
(ii) a second channel configured to receive a second fluid that is immiscible with the first fluid;
(iii) a third channel; and
(iv) a droplet generation junction connected to the first channel, the second channel, and the third channel; 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 microcapsules of the plurality of microcapsules flow along the first channel to the droplet generation junction, and
(ii) subjecting the second fluid to flow along the second channel towards the droplet generation junction, wherein the first fluid and the second fluid meet at the droplet generation junction to generate a plurality of droplets comprising the microcapsules of the plurality of microcapsules, which plurality of droplets flow along the third channel.

US Pat. No. 10,347,365

SYSTEMS AND METHODS FOR VISUALIZING A PATTERN IN A DATASET

10X GENOMICS, INC., Plea...

1. A visualization system, the visualization system comprising one or more processing cores, a persistent memory and a non-persistent memory, the persistent memory and the non-persistent memory collectively storing instructions for performing a method for visualizing a pattern in a discrete attribute value dataset, the method comprising:storing the discrete attribute value dataset in persistent memory, wherein
the discrete attribute value dataset comprises a corresponding discrete attribute value for each first entity in a plurality of first entities for each respective second entity in a plurality of second entities, and
the discrete attribute value dataset redundantly represents the corresponding discrete attribute value for each first entity in the plurality of first entities for each respective second entity in the plurality of second entities in both a compressed sparse row format and a compressed sparse column format in which first entities for a respective second entity that have a null discrete attribute data value are discarded,
the discrete attribute value dataset is compressed in accordance with a blocked compression algorithm;
clustering the discrete attribute value dataset using the discrete attribute value for each first entity in the plurality of first entities, or principal components derived therefrom, for each respective second entity in the plurality of second entities thereby assigning each respective second entity in the plurality of second entities to a corresponding cluster in a plurality of clusters, wherein
each respective cluster in the plurality of clusters consists of a unique different subset of the second plurality of entities, and
the clustering loads less than the entirety of the discrete attribute value dataset into the non-persistent memory at any given time during the clustering, thereby allowing the clustering of the discrete attribute value dataset having a size that exceeds storage space in the non-persistent memory allocated to the discrete attribute value dataset;
computing, for each respective first entity in the plurality of first entities for each respective cluster in the plurality of clusters, a difference in the discrete attribute value for the respective first entity across the respective subset of second entities in the respective cluster relative to the discrete attribute value for the respective first entity across the plurality of clusters other than the respective cluster, thereby deriving a differential value for each respective first entity in the plurality of first entities for each respective cluster in the plurality of clusters; and
displaying in a first panel a heat map that comprises a representation of the differential value for each respective first entity in the plurality of first entities for each cluster in the plurality of clusters thereby visualizing the pattern in the discrete attribute value dataset.
US Pat. No. 10,400,235

SINGLE CELL ANALYSIS OF TRANSPOSASE ACCESSIBLE CHROMATIN

10X GENOMICS, INC., Plea...

1. A method of generating barcoded nucleic acid fragments, comprising:(a) generating a plurality of partitions, wherein at least a subset of said plurality of partitions comprises: (i) a single biological particle from a plurality of biological particles, wherein said single biological particle comprises template deoxyribonucleic acid (DNA) molecules and template ribonucleic acid (RNA) molecules; (ii) a plurality of first barcode oligonucleotide molecules comprising a first barcode sequence; (iii) a plurality of transposon end oligonucleotide molecules comprising a transposon end sequence; (iv) a plurality of transposase molecules; (v) a plurality of second barcode oligonucleotide molecules comprising a second barcode sequence and a capture sequence; and (vi) a plurality of reverse transcriptase molecules;
(b) generating a plurality of template DNA fragments by subjecting said subset of said plurality of partitions to conditions sufficient to cause transposition of said transposon end oligonucleotide molecules into said template DNA molecules with the aid of a transposase-nucleic acid complex comprising a transposase molecule of said plurality of transposase molecules and a transposon end oligonucleotide molecule of said plurality of transposon end oligonucleotide molecules;
(c) generating a barcoded DNA fragment using a first barcode oligonucleotide molecule of said plurality of first barcode oligonucleotide molecules and a template DNA fragment of said plurality of template DNA fragments; and
(d) generating a barcoded complementary DNA molecule from said template RNA molecules by reverse transcription using a second barcode oligonucleotide molecule of said plurality of second barcode oligonucleotide molecules.
US Pat. No. 10,392,662

METHODS FOR ANALYZING NUCLEIC ACIDS FROM SINGLE CELLS

10X GENOMICS, INC., Plea...

1. A composition for multiplexed nucleic acid analysis, comprising:a plurality of beads, wherein the beads are covalently attached to a plurality of oligonucleotide tags, and wherein an oligonucleotide tag of said plurality of oligonucleotide tags comprises:
(a) a first tag sequence configured to distinguish a sample polynucleotide originating from a cell from sample polynucleotides originating from other cells; and
(b) a second tag sequence configured to distinguish said sample polynucleotide from other sample polynucleotide from the same cell and having the same sequence as said sample polynucleotide.
US Pat. No. 10,344,329

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for cellular analysis, comprising:(a) causing an analyte of a cell to contact a cell feature binding group to provide said cell feature binding group coupled to said analyte, wherein said cell feature binding group is associated with a first nucleic acid molecule comprising a first barcode sequence; and
(b) using said first nucleic acid molecule and a second nucleic acid molecule to generate a third nucleic acid molecule, wherein said second nucleic acid molecule comprises a second barcode sequence, and wherein said third nucleic acid molecule comprises (i) said first barcode sequence or complement thereof, and (ii) said second barcode sequence or complement thereof.
US Pat. No. 10,337,061

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for nucleic acid sequencing, comprising:(a) co-partitioning a plurality of beads and a plurality of primers in a plurality of droplets, wherein a droplet of said plurality of droplets comprises (i) a ribonucleic acid (RNA) molecule comprising a nucleic acid sequence, (ii) a primer from said plurality of primers, and (iii) a bead from said plurality of beads, wherein said bead comprises a nucleic acid barcode molecule coupled thereto, and wherein said nucleic acid barcode molecule comprises a barcode sequence;
(b) hybridizing said primer to a region at a 3? end of said RNA molecule;
(c) using an enzyme to extend said primer to generate a nucleic acid product comprising a sequence corresponding to said nucleic acid sequence of said RNA molecule, wherein said enzyme incorporates an end sequence at a 3? end of said nucleic acid product that is complementary to said nucleic acid barcode molecule;
(d) hybridizing said nucleic acid barcode molecule to said nucleic acid product generated in (c) and extending said nucleic acid product using said nucleic acid barcode molecule as a template, to generate a barcoded nucleic acid molecule comprising, from a 5? end to a 3? end, (1) said sequence corresponding to said nucleic acid sequence of said RNA molecule and (2) a complement of said barcode sequence; and
(e) sequencing said barcoded nucleic acid molecule or derivative thereof,
wherein, after (a), said nucleic acid barcode molecule is released from said bead.
US Pat. No. 10,337,063

METHODS FOR ANALYZING NUCLEIC ACIDS FROM SINGLE CELLS

10X GENOMICS, INC., Plea...

1. An array for multiplexed nucleic acid analysis, comprising:a solid support having a plurality of beads disposed thereon, wherein the beads are covalently attached to a plurality of oligonucleotide tags, and wherein an oligonucleotide tag of said plurality of oligonucleotide tags comprises:
(a) a first tag sequence configured to distinguish a sample polynucleotide originating from a cell from sample polynucleotides originating from other cells; and
(b) a second tag sequence configured to distinguish said sample polynucleotide from other sample polynucleotide from the same cell and having the same sequence as said sample polynucleotide.
US Pat. No. 10,280,459

METHODS FOR ANALYZING NUCLEIC ACIDS FROM SINGLE CELLS

10X GENOMICS, INC., Plea...

1. A method for multiplexed analysis of nucleic acids from single cells, the method comprising:(a) providing a sample comprising a plurality of cells, wherein a single cell of the plurality of cells comprises a plurality of sample polynucleotides;
(b) performing primer extension to generate a plurality of tagged polynucleotides from said plurality of sample polynucleotides and a plurality of oligonucleotide tags, wherein a tagged polynucleotide of the plurality of tagged polynucleotides comprises:
(i) a sample sequence from a sample polynucleotide of the plurality of sample polynucleotides;
(ii) a first tag sequence distinguishing said sample polynucleotide from sample polynucleotides originating from other single cells; and
(iii) a second tag sequence distinguishing said sample polynucleotide from other sample polynucleotides originating from said same single cell;
(c) amplifying said tagged polynucleotide, thereby generating a plurality of amplified polynucleotides; and
(d) sequencing said plurality of amplified polynucleotides to determine sequences of the amplified polynucleotides corresponding to the sample sequence, the first tag sequence, and the second tag sequence of the tagged polynucleotide; and
(e) using the sequences determined in step (d) to count sample polynucleotides for multiple different sample polynucleotides of multiple different single cells of said plurality of cells.
US Pat. No. 10,400,280

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method of single cell gene expression analysis, comprising:(a) providing a plurality of beads, wherein a bead of said plurality of beads comprises a plurality of nucleic acid barcode molecules each comprising:
(i) a common barcode sequence configured to identify a cellular origin of mRNA molecules; and
(ii) an identification barcode sequence configured to quantify mRNA molecules;
(b) partitioning a plurality of cells and said plurality of beads in a system comprising a plurality of partitions, wherein said system comprises 1,000 occupied partitions each comprising a single cell of said plurality of cells and a single bead of said plurality of beads, wherein different occupied partitions have different common barcode sequences;
(c) releasing mRNA molecules from single cells of said 1,000 occupied partitions;
(d) using said plurality of nucleic acid barcode molecules to generate a plurality of barcoded nucleic acid molecules from the mRNA molecules released in (c), wherein a barcoded nucleic acid molecule of said plurality of barcoded nucleic acid molecules comprises: (i) a sequence of an mRNA molecule of said released mRNA molecules, or a reverse complement of said sequence of said mRNA molecule; and (ii) a sequence of a nucleic acid barcode molecule of said plurality of nucleic acid barcode molecules, including said common barcode sequence and said identification barcode sequence, or a reverse complement of said sequence of said nucleic acid barcode molecule;
(e) determining sequences of said plurality of barcoded nucleic acid molecules;
(f) using common barcode sequences from said sequences determined in (e) to identify cellular origins of said plurality of barcoded nucleic acid molecules, thereby identifying cellular origins of said mRNA molecules from which said plurality of barcoded nucleic acid molecules were generated; and
(g) using identification barcode sequences from said sequences determined in (e) to identify molecular origins of said plurality of barcoded nucleic acid molecules, thereby quantifying said mRNA molecules from which said plurality of barcoded nucleic acid molecules were generated.
US Pat. No. 10,323,279

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for polynucleotide barcoding, comprising:(a) providing a first set of partitions comprising (i) a first set of nucleic acid barcode molecules comprising barcode sequences and (ii) a plurality of polynucleotides and attaching said first set of nucleic acid barcode molecules to said plurality of polynucleotides to generate a first set of barcoded polynucleotides;
(b) pooling contents of said first set of partitions;
(c) partitioning (i) a second set of nucleic acid barcode molecules comprising barcode sequences and (ii) at least a portion of said contents from (b) into a second set of partitions different than said first set of partitions; and
(d) in said second set of partitions, attaching said second set of nucleic acid barcode molecules to said first set of barcoded polynucleotides to generate a second set of barcoded polynucleotides.
US Pat. No. 10,395,758

SEQUENCING METHODS

10X GENOMICS, INC., Plea...

1. A method of processing a plurality of nucleic acid molecules derived from a biological sample of a subject comprising:(a) obtaining said plurality of nucleic acid molecules derived from the biological sample of said subject;
(b) using a sequencer to sequence said plurality of nucleic acid molecules to generate a set of partial sequencing reads comprising a first partial sequencing read having a first barcode sequence;
(c) while said sequencer is sequencing said plurality of nucleic acid molecules in (b), streaming said set of partial sequencing reads over a network to a sequencing analysis system remotely located with respect to said sequencer; and
(d) while said sequencer is sequencing said plurality of nucleic acid molecules in (b), using said sequencing analysis system to (i) assign said first partial sequencing read to a given group of a plurality of groups based on said first barcode sequence, (ii) correct a sequencing error identified based on a frequency of a subsequence occurring among partial sequencing reads of said given group, and (iii) assemble said first sequencing read with other reads of said set of partial sequencing reads.
US Pat. No. 10,366,777

SYSTEMS AND METHODS FOR DETERMINING THE INTEGRITY OF TEST STRINGS WITH RESPECT TO A REFERENCE GENOME

10X GENOMICS, INC., Plea...

1. A computing system comprising:one or more processors; and
memory, the memory storing one or more programs to be executed by the one or more processors, the one or more programs comprising instructions for determining whether a sequence event arises between a first and a second position in a first string or a second string using a reference genome through a two phase method, wherein
the reference genome encompasses an entirety of the first string and an entirety of the second string,
the first string is not fully determined,
the second string is not fully determined, andthe two phase method comprises:(A) obtaining a data construct representing a plurality of components, wherein
each respective component in the plurality of components maps to a different contiguous portion of the reference genome and represents less than one percent of the reference genome,
the data construct comprises a plurality of sequence read pools,
each sequence read pool (i) has a different identifier in a plurality of identifiers and (ii) comprises a corresponding plurality of sequence reads,
each respective sequence read in the corresponding plurality of sequence reads of a sequence read pool in the plurality of sequence read pools (i) is obtained from an optical measurement device and (ii) includes the same identifier string in addition to a coding string that consists of a portion of the first string or the second string,
each respective sequence read in the plurality of sequence reads of a sequence read pool in the plurality of sequence read pools is assigned to (i) a first class when the coding region of the respective sequence read matches a portion of the first string, (ii) a second class when the coding region of the respective sampling matches a portion of the second string or (iii) a third class when the coding region of the respective sequence read matches the portion of the first string as well as the portion of the second string,
the plurality of sequence reads across each respective sequence read pool in the plurality of sequence read pools collectively forms a Poisson or near Poisson distribution of sequence reads across both the first string and the second string,
at least some of the sequence reads in the plurality of sequence read pools have not been assigned to the first class, the second class, or the third class with absolute certainty,
each plurality of sequence reads represents one or two corresponding components in the plurality of components;
the data construct does not include sequence reads for at least a predetermined portion of each component in the plurality of components;
(B) identifying first and second positions in the reference genome;
(C) calculating, as part of a first phase of the two phase method, an initial basis of the sequence event arising between the first and second positions in the first or second string using each of a plurality of models and an initial assumption of the number of components that contribute to each pool of sequence reads that includes sequence reads that collectively encompass the first position or the second position and (ii) the class assignment of the sequence reads that map onto components that overlap the first position or the second position, wherein each model in the plurality of models posits an observed distribution of sequence reads in the data construct across the portion of the reference genome that is bounded by the first position and the second position against an expected distribution of sequence reads in the construct across the reference genome upon introduction of a sequence event, wherein
a first model in the plurality of models assumes that no sequence event occurs between the first position and the second position in the first string or the second string,
a second model in the plurality of models assumes that a sequence event occurs between the first position and the second position in both the first string and the second string, and
a third model in the plurality of models assumes that a sequence event occurs between the first position and the second position in only one of the first string and the second string but not the other of the first string and the second string;
(D) adjusting, as part of the second phase of the two phase method, the initial assumption of (i) the number of components that contribute to each pool of sequence reads that includes sequence reads that map to components that overlap the first position or the second position and (ii) the class assignment of the sequence reads that map onto components that overlap the first position or the second position using the calculated basis of the sequence event arising between the first position and the second position in the first string or the second string from each of the plurality of models using an expectation-maximization algorithm; and
(E) repeating the calculating (C) and adjusting (D) until a convergence criterion is satisfied thereby determining whether the first string or the second string have a structural variation with respect to the reference genome.
US Pat. No. 10,323,278

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for analyte characterization, comprising:(a) providing a plurality of partitions, wherein a partition of said plurality of partitions comprises a plurality of analytes derived from a cell and a plurality of barcode molecules coupled to a bead, wherein said plurality of barcode molecules comprises:
(i) a first barcode molecule comprising a nucleic acid barcode sequence, wherein said first barcode molecule is configured to couple to a first analyte of said plurality of analytes or a derivative generated from said first analyte, wherein said first analyte is a clustered regularly interspaced short palindromic repeat (CRISPR) ribonucleic acid (crRNA) or a single guide ribonucleic acid (sgRNA), and
(ii) a second barcode molecule comprising said nucleic acid barcode sequence, wherein said second barcode molecule is configured to couple to a second analyte of said plurality of analytes or a derivative generated from said second analyte;
(b) in said partition, (i) coupling said first barcode molecule to said first analyte or derivative thereof, and synthesizing a first barcoded nucleic acid molecule comprising said nucleic acid barcode sequence or a complement thereof and a sequence of at least a portion of said first analyte or complement thereof; and (ii) coupling said second barcode molecule to said second analyte or derivative thereof, and synthesizing a second barcoded nucleic acid molecule comprising said nucleic acid barcode sequence or complement thereof and a sequence of at least a portion of said second analyte or complement thereof;
(c) processing (i) said first barcoded nucleic acid molecule or derivative thereof and (ii) said second barcoded nucleic acid molecule or derivative thereof, to identify said nucleic acid barcode sequence; and
(d) using said nucleic acid barcode sequence to correlate said first analyte and said second analyte with said cell.
US Pat. No. 10,370,711

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for analyzing cells comprising:(a) contacting a plurality of cells with an antibody to provide a cell bound to said antibody, wherein said antibody is attached to a reporter oligonucleotide comprising a reporter sequence;
(b) co-partitioning at least a subset of said plurality of cells into a plurality of wells, wherein a well of said plurality of wells comprises (i) said cell bound to said antibody and (ii) a first nucleic acid molecule comprising a barcode sequence; and
(c) using said reporter oligonucleotide and said first nucleic acid molecule to generate a second nucleic acid molecule comprising (i) said reporter sequence, and (ii) said barcode sequence.

US Pat. No. 10,357,771

METHOD OF PRODUCING EMULSIONS

10X Genomics, Inc., Plea...

1. A method of producing droplets comprising:a) providing a device comprising:
i) a first channel having a first proximal end, a first distal end, a first depth, and a first width, the first channel comprising a first liquid;
ii) a second channel having a second proximal end, a second distal end, a second depth, and a second width; wherein the second channel intersects the first channel between the first proximal end and the first distal end, the second channel comprising a third liquid;
iii) a droplet formation region in fluid communication with the first distal end of the first channel, wherein the droplet formation region has a width or depth greater than the first width or first depth and the droplet formation region comprises a second liquid; and
iv) a collection region in fluid communication with the droplet formation region and that collects droplets formed in the droplet formation region;
wherein the first liquid is immiscible with the second liquid, wherein the first or third liquid comprises one or more particles and wherein the device is capable of forming droplets with the second liquid flowing in response to displacement by the droplets being formed;
b) flowing the first liquid from the first channel and the third liquid from the second channel to the intersection to combine the first and third liquids;
c) flowing the combined first and third liquids to the droplet formation region to produce droplets of the first liquid, third liquid, and one or more particles dispersed in the second liquid;
d) transporting the droplets to the collection region; and
e) collecting the droplets in the collection region.
US Pat. No. 10,428,326

METHODS AND SYSTEMS FOR DROPLET-BASED SINGLE CELL BARCODING

10X GENOMICS, INC., Plea...

1. A method for processing or analyzing one or more components from a cellular sample, comprising:(a) providing a plurality of cell beads and a plurality of barcode beads, wherein (i) a cell bead of said plurality of cell beads comprises a cell, wherein said cell comprises a nucleic acid molecule in an interior region of said cell, and (ii) a barcode bead of said plurality of barcode beads comprises a plurality of nucleic acid barcode molecules, wherein nucleic acid barcode molecules of said plurality of nucleic acid barcode molecules comprise a common barcode sequence;
(b) subjecting said plurality of cell beads to bulk processing, which bulk processing comprises: (i) rendering said nucleic acid molecule accessible to a species external to said interior region and (ii) denaturing said nucleic acid molecule to generate a denatured nucleic acid molecule in said cell bead; and
(c) partitioning said plurality of cell beads and said plurality of barcode beads into a plurality of partitions, wherein upon partitioning, a partition of said plurality of partitions comprises said cell bead and said barcode bead.
US Pat. No. 10,457,986

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A method for analyzing analytes comprising:(a) providing a first analyte, a second analyte, a cell feature binding group comprising a reporter molecule comprising a reporter barcode sequence associated with said cell feature binding group, and a support having coupled thereto a plurality of nucleic acid barcode molecules,
wherein said second analyte is a different type of analyte than said first analyte,
wherein said cell feature binding group is configured to couple to said first analyte, and
wherein said plurality of nucleic acid barcode molecules comprise (i) a common barcode sequence and (ii) a common capture sequence; and
(b) generating:
(i) a first barcoded nucleic acid molecule comprising: (1) a first sequence corresponding to said reporter barcode sequence and (2) a second sequence corresponding to said common barcode sequence, and
(ii) a second barcoded nucleic acid molecule comprising: (1) a third sequence corresponding to said second analyte and (2) a fourth sequence corresponding to said common barcode sequence.

US Pat. No. 10,452,448

SYSTEMS AND METHODS FOR DISTRIBUTED RESOURCE MANAGEMENT

10X Genomics, Inc., Plea...

1. A computing system comprising one or more processors and a memory, the memory storing one or more programs for execution by the one or more processors, the one or more programs singularly or collectively comprising instructions for executing a method comprising:for a plurality of jobs in a queue, wherein each respective job in the plurality of jobs is associated with a timestamp that indicates when the respective job was submitted to the queue and specifies one or more node resource requirements:
(A) determining a composite hardware requirement, for the plurality of jobs, from the one or more node resource requirements of each job in the plurality of jobs;
(B) identifying one or more nodes to add to a cluster to satisfy at least a subset of the composite hardware requirements, wherein the identifying (B) comprises:
(i) obtaining a current availability score or list price for each respective node class in a plurality of node classes, and
(ii) submitting a request for one or more nodes of a corresponding node class in the plurality of node classes when a demand score for the corresponding node class (a) satisfies the current availability score for the corresponding node class by a first threshold amount or (b) satisfies the list price for the corresponding node class;
(C) adding the one or more nodes to the cluster of nodes, wherein the adding comprises installing a distributed computing module on each respective node in the one or more nodes; and
(D) granting each respective node in the one or more nodes with a draw privilege, wherein the draw privilege permits the distributed computing module of a respective node to draw one or more jobs from the plurality of jobs subject to a constraint that the collective hardware requirements of the one or more jobs collectively drawn by a respective node in the cluster of nodes does not exceed the hardware resources of the respective node, and wherein the respective node identifies the one or more jobs by scanning the plurality of jobs in accordance with the draw privilege.
US Pat. No. 10,450,607

METHODS AND SYSTEMS FOR PROCESSING POLYNUCLEOTIDES

10X GENOMICS, INC., Plea...

1. A system for nucleic acid processing or analysis, comprising:(a) a plurality of antibody-oligonucleotide conjugates, wherein an antibody-oligonucleotide conjugate of said plurality of antibody-oligonucleotide conjugates comprises an antibody and an oligonucleotide reporter molecule comprising a reporter barcode sequence, and wherein said reporter barcode sequence identifies said antibody;
(b) a plurality of beads comprising a plurality of barcode sequences, wherein a bead of said plurality of beads comprises a plurality of nucleic acid barcode molecules comprising a common barcode sequence; and
(c) a microwell array comprising 1,000 microwells, wherein said microwell array is configured to partition a plurality of cells and said plurality of beads into microwells of said microwell array, wherein a microwell of said microwell array comprises: (i) a single cell of said plurality of cells; and (ii) said bead, and wherein said single cell is bound to said antibody-oligonucleotide conjugate.