PALO ALTO, CA, United States
PALO ALTO, CA, United States

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Patent
Cellular Research, Inc. | Date: 2016-09-08

The disclosure provides for methods, compositions, and kits for normalizing nucleic acid libraries, for example sequencing libraries.


Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.


Patent
Cellular Research, Inc. | Date: 2016-05-27

The disclosure provides for methods, compositions, and kits for multiplex nucleic acid analysis of single cells. The methods, compositions and systems may be used for massively parallel single cell sequencing. The methods, compositions and systems may be used to analyze thousands of cells concurrently. The thousands of cells may comprise a mixed population of cells (e.g., cells of different types or subtypes, different sizes).


Patent
Cellular Research, Inc. | Date: 2016-03-29

The present disclosure provide compositions, methods and kits for generating a set of combinatorial barcodes, and uses thereof for barcoding samples such as single cells or genomic DNA fragments. Some embodiments disclosed herein provide compositions comprising a set of component barcodes for producing a set of combinatorial barcodes. The set of component barcodes can comprise, for example, nm unique component barcodes, wherein n and m are integers, each of the component barcodes comprises: one of n unique barcode subunit sequences; and one or two linker sequences or the complements thereof, wherein the component barcodes are configured to connect to each other through the one or two linker sequences or the complements thereof to produce a set of combinatorial barcodes.


Patent
Cellular Research, Inc. | Date: 2016-02-26

The disclosure provides for methods, compositions, systems, devices, and kits for determining the number of distinct targets in distinct spatial locations within a sample. In some examples, the methods include: stochastically barcoding the plurality of targets in the sample using a plurality of stochastic barcodes, wherein each of the plurality of stochastic barcodes comprises a spatial label and a molecular label; estimating the number of each of the plurality of targets using the molecular label; and identifying the spatial location of each of the plurality of targets using the spatial label. The method can be multiplexed.


Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.


Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample.


Patent
Cellular Research, Inc. | Date: 2016-04-21

The disclosure provides for methods, compositions, systems, devices, and kits for whole transcriptome amplification using stochastic barcodes.


Grant
Agency: Department of Health and Human Services | Branch: National Institutes of Health | Program: SBIR | Phase: Phase II | Award Amount: 1.51M | Year: 2015

DESCRIPTION provided by applicant A kit for massively parallel single cell gene expression analysis Abstract Interest in single cell gene expression analysis harnessing the capability of next generation sequencing NGS has recently gained momentum in the academic community Although sequencing has become cheaper the ability to measure gene expression profile at the single cell level is extremely constrained by the limitation of technolog for preparing sequencing libraries from single cells Currently available sample preparation techniques require expensive instruments and are brute force and low throughput Single cell gene expression would be much more powerful if it can be scaled to examine tens of thousands of cells at a time and across many genes Not only will such technology advance our knowledge in basic biology and medicine it also has many potential clinical applications We have recently developed a low cost and high resolution massively parallel method to prepare sequencing libraries from large number of single cells for gene expression analysis The method is based on the concept of stochastic labeling executed at the single cell and the single molecule level We have successfully conducted expression analysis of genes of close to single cells per sample routinely and have demonstrated the ability of our system to classify major cell types in heterogeneous cell mixtures such as human blood The scalability throughput and economy of our technology far exceed existing commercial platforms For this proposed Phase II project we plan to further scale our technology to enable routine analysis of hundreds of genes across cells per sample and to convert the current working prototype into an exportable product that includes a reagent kit a simple reagent loading device and supporting assay design and analysis software PUBLIC HEALTH RELEVANCE A kit for massively parallel single cell gene expression analysis Narrative We aim to develop a commercial kit that enables low cost routine sequencing based digital gene expression measurement of or more individual cells in a biological sample Our technology would widen the adoption of large scale single cell analysis by researchers enabling researchers to gain better understanding of complex biological systems and their relationships to health and diseases It also has a number of potential clinical applications especially in situations when identification of rare cells is crucial Examples inclue early cancer detection monitoring of cancer therapy and evaluating responses to drugs and vaccines


Patent
Cellular Research, Inc. | Date: 2016-02-26

Embodiments provided herein relate to methods and compositions for labeling a nucleic acid in a sample with a stochastic barcode. Some embodiments relate to methods and compositions for characterizing a sample by identifying the TCR alpha chain or beta chain of a T cell.

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