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    SYSTEMS AND METHODS FOR CORRECTING SAMPLE PREPARATION ARTIFACTS IN DROPLET-BASED SEQUENCING
    3.
    发明申请
    SYSTEMS AND METHODS FOR CORRECTING SAMPLE PREPARATION ARTIFACTS IN DROPLET-BASED SEQUENCING 有权

    公开(公告)号：US20210324454A1

    公开(公告)日：2021-10-21

    申请号：US17232058

    申请日：2021-04-15

    Applicant: 10x Genomics, Inc.

    Inventor： Preyas Shah ,  Li Wang ,  Brett Olsen

    IPC: C12Q1/6816 ,  C12Q1/6858 ,  C12Q1/683

    Abstract: A method for filtering open chromatin regions on a cell barcode genomic sequence dataset is provided, comprising receiving, by one or more processors, a cell barcode genomic sequence dataset, the method comprising a plurality of fragment sequence reads and barcodes associated with the plurality of fragment sequence reads. The method further comprising generating, by the one or more processors, an adjacency matrix that counts up pairs of adjacent fragment sequence reads and barcodes associated with each fragment sequence read. The method further comprising identifying, by the one or more processors, pairs of adjacent fragment sequence reads with different barcodes and annotating the pair as a multiplet pair. The method further comprising filtering, by the one or more processors, one fragment sequence read from each of the identified multiplet pairs. The method further comprising generating, by the one or more processors, a multiplet filtered cell barcode genomic sequence dataset.

    SYSTEMS AND METHODS FOR VISUALIZING A PATTERN IN A DATASET
    4.
    发明申请
    SYSTEMS AND METHODS FOR VISUALIZING A PATTERN IN A DATASET 审中-公开

    公开(公告)号：US20190332963A1

    公开(公告)日：2019-10-31

    申请号：US16442800

    申请日：2019-06-17

    Applicant: 10X Genomics, Inc.

    Inventor： Alexander Y. Wong ,  Jeffrey Mellen ,  Kevin J. Wu ,  Paul Ryvkin ,  Preyas Shah ,  Patrick Marks ,  Niranjan Srinivas

    IPC: G06N7/00 ,  G06F16/28 ,  G06F16/904

    Abstract: A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.

    RESOLVING SPATIAL ARRAYS USING DECONVOLUTION
    6.
    发明申请
    RESOLVING SPATIAL ARRAYS USING DECONVOLUTION 有权

    公开(公告)号：US20220290217A1

    公开(公告)日：2022-09-15

    申请号：US17312615

    申请日：2019-12-06

    Applicant: 10x Genomics, Inc.

    Inventor： Lucas Frenz ,  Preyas Shah ,  Benjamin Hindson ,  Eswar Prasad Ramachandran Iyer

    IPC: C12Q1/6837 ,  C12N15/10

    Abstract: Methods for determining a location of a feature on an array include: (a) providing a first array with a first plurality of features immobilized on a first substrate; (b) providing a second array with a second plurality of features immobilized on a second substrate; (c) aligning the first array with the second array; (d) hybridizing a first barcoded oligonucleotide of the first array to a second barcoded oligonucleotide of the second array, thereby producing a combined nucleic acid that includes first and second spatial barcodes; (e) determining all or a portion of the sequence of the combined nucleic acid; and (f) identifying the second barcoded oligonucleotide associated with the first barcoded oligonucleotide in the combined nucleic acid, and determining the location of a second feature in the second array.

    SPECTRAL UNMIXING COMBINED WITH DECODING FOR SUPER-MULTIPLEXED IN SITU ANALYSIS
    7.
    发明公开
    SPECTRAL UNMIXING COMBINED WITH DECODING FOR SUPER-MULTIPLEXED IN SITU ANALYSIS 审中-公开

    公开(公告)号：US20240305314A1

    公开(公告)日：2024-09-12

    申请号：US18660149

    申请日：2024-05-09

    Applicant: 10x Genomics, Inc.

    Inventor： David HOFFMAN ,  Denis Pristinski ,  Elijah Roberts ,  Preyas Shah

    IPC: H03M13/37 ,  G01N21/64

    CPC classification number: H03M13/3753 ,  G01N21/6456 ,  G01N2021/6471

    Abstract: Techniques for spectral unmixing and decoding for in situ analysis are provided. Input hypercube data comprising voxel data, raw channel data, and decoding round data are obtained, and an initial iteration of codeword data determination is performed. Performing the initial iteration includes generating initial feature data and initial unmixed fluorescence data, generating initial uncorrected codeword data, and generating initial corrected codeword data. One or more subsequent iterations of codeword data determination are then performed based on the input hypercube data and based on feature data, unmixed fluorescence data, uncorrected codeword data, and corrected codeword data from one or more previous iterations. When it is determined that one or more convergence conditions have been satisfied, output comprising an optimized estimate of fluorescence data, and an optimized estimate of uncorrected codeword data, and an optimized estimate of corrected codeword data is generated.

    SYSTEMS AND METHODS FOR SPATIAL ANALYSIS OF ANALYTES USING FIDUCIAL ALIGNMENT
    9.
    发明申请
    SYSTEMS AND METHODS FOR SPATIAL ANALYSIS OF ANALYTES USING FIDUCIAL ALIGNMENT 有权

    公开(公告)号：US20210158522A1

    公开(公告)日：2021-05-27

    申请号：US16951843

    申请日：2020-11-18

    Applicant: 10X Genomics, Inc.

    Inventor： Neil Ira Weisenfeld ,  Narek Dshkhunyan ,  Preyas Shah

    IPC: G06T7/00 ,  G06T7/136 ,  G06T3/00 ,  G06T3/60 ,  G06K9/62 ,  G16B25/00

    Abstract: Systems and methods for spatial analysis of analytes are provided. A data structure is obtained comprising an image, as an array of pixel values, of a sample on a substrate having a identifier, fiducial markers and a set of capture spots. The pixel values are used to identify derived fiducial spots. The substrate identifier identifies a template having reference positions for reference fiducial spots and a corresponding coordinate system. The derived fiducial spots are aligned with the reference fiducial spots using an alignment algorithm to obtain a transformation between the derived and reference fiducial spots. The transformation and the template corresponding coordinate system are used to register the image to the set of capture spots. The registered image is then analyzed in conjunction with spatial analyte data associated with each capture spot, thereby performing spatial analysis of analytes.

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