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：US20220076780A1

公开(公告)日：2022-03-10

申请号：US17465682

申请日：2021-09-02

Applicant: 10x Genomics, Inc.

Inventor： Arundhati Shamoni Maheshwari ,  Vijay Kumar Sreenivasa Gopalan ,  Brett Olsen ,  Nicolaus Lance Hepler

IPC: G16B20/00 ,  G16B40/00

Abstract: Methods and systems may be provided for distinguishing cell populations from non-cell populations within a data set, the method comprising receiving a data set at least associated with a plurality of cells, wherein the data set comprises molecule counts of at least two genomic features for each cell; identifying duplicate subsets of data points from the data set; generating deduplicated data by condensing data points from each duplicate subset into a single data point; applying a pre-set threshold to divide the deduplicated data into an initial cell population and a non-cell population, wherein the pre-set threshold is determined using the molecule counts; and generating a refined cell population and a non-cell population by adjusting boundaries of the initial cell population and non-cell population using clustering.

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.