公开(公告)号：US20210381056A1

公开(公告)日：2021-12-09

申请号：US17175577

申请日：2021-02-12

Applicant: 10X Genomics, Inc.

Inventor： Jessica Hamel ,  Vijay Kumar Sreenivasa Gopalan ,  Li Wang ,  Arundhati Shamoni Maheshwari ,  Jasper Staab

IPC: C12Q1/6886 ,  G16B40/00 ,  G16B15/00 ,  G16B5/20

Abstract: Systems and methods for visualizing patterns in discrete attribute value datasets are provided. A dataset comprises a discrete attribute value for each gene in a plurality of genes, for each cell in a plurality of cells. The dataset further comprises ATAC counts for each ATAC peak in a plurality of peaks, for each of the cells. Cells are assigned cluster groups in a first plurality of cluster groups based on a first clustering of discrete attribute values for the genes across the cells. Cell are also assigned cluster groups in a second plurality of cluster groups based on a second clustering of ATAC fragment count values for the ATAC peaks across the cells. A projection of the cells uses one of the first or second cluster group assignments. There is indicated, for each cell within the projection, membership in the other of the first or second cluster group assignments.

公开(公告)号：US20210332354A1

公开(公告)日：2021-10-28

申请号：US17231972

申请日：2021-04-15

Applicant: 10x Genomics, Inc.

Inventor： Preyas Shah ,  Li Wang ,  Brett Olsen

IPC: C12N15/10 ,  C12Q1/6806 ,  C12Q1/6876 ,  G16B30/10

Abstract: A method for ascertaining differential accessibility of (TF) binding motifs in open chromatin regions of cells, comprising receiving a cell barcode genomic sequence dataset; aligning each of a plurality of fragment sequence reads to a reference sequence; identifying peaks defined by the aligned plurality of fragment sequence reads; generating a peak-barcode matrix that is comprised of peaks for each cell barcode; clustering cells with peaks having similar chromatin accessibility profiles into a cell cluster to form one or more cell clusters; generating a TF barcode matrix that maps each peak in the peak-barcode matrix to one or more given TF binding motif(s); performing a differential accessibility analysis, wherein the analysis identifies differences in accessibility of peaks and TF binding motifs associated with each identified cell cluster relative to all other identified cell clusters; and generating an output of one or more refined cell clusters based on the differential accessibility analysis.

公开(公告)号：US20220076784A1

公开(公告)日：2022-03-10

申请号：US17465725

申请日：2021-09-02

Applicant: 10x Genomics, Inc.

Inventor： Li Wang ,  Yiming Kang

IPC: G16B20/40

Abstract: Methods and systems for generating linkage correlations and linkage significances between a first genomic feature and a second genomic feature identified for each of a plurality of cells may be provided. For example, the method may comprise receiving a data matrix comprising a first genomic feature and a second genomic feature identified for each of a plurality of cells; smoothing the data matrix to generate a smoothed matrix; generating linkage correlations between the first genomic feature and second genomic feature identified for each of the plurality of cells in the data matrix; generating linkage significances using multiplication of a plurality of linkage matrixes; and outputting the linkage correlations and linkage significances for each of the plurality of cells in the data matrix.

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.