公开(公告)号：US20200277663A1

公开(公告)日：2020-09-03

申请号：US16876913

申请日：2020-05-18

Applicant: 10x Genomics, Inc.

Inventor： Eswar Prasad Ramachandran Iyer ,  Tarjei Sigurd Mikkelsen ,  Preyas Shah

IPC: C12Q1/6844 ,  C12Q1/6841 ,  C12Q1/6876 ,  C12Q1/6874

Abstract: Provided herein are methods of determining a location of a biological analyte in a biological sample.

公开(公告)号：US12229974B2

公开(公告)日：2025-02-18

申请号：US18046404

申请日：2022-10-13

Applicant: 10x Genomics, Inc.

Inventor： Neil Ira Weisenfeld ,  Narek Dshkhunyan ,  Preyas Shah

IPC: G06T7/33 ,  G06F18/22 ,  G06T3/147 ,  G06T3/608 ,  G06T7/00 ,  G06T7/136 ,  G06V20/69 ,  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.

公开(公告)号：US11501440B2

公开(公告)日：2022-11-15

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 ,  G16B25/00 ,  G06K9/62 ,  G06T3/00 ,  G06T3/60

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.

公开(公告)号：US11365438B2

公开(公告)日：2022-06-21

申请号：US15930120

申请日：2020-05-12

Applicant: 10X GENOMICS, INC.

Inventor： Daniel P. Riordan ,  Preyas Shah ,  Michael Schnall-Levin

IPC: C12Q1/6806 ,  C12N15/10

Abstract: The present disclosure provides methods and systems for nucleic acid preparation and analysis. Nucleic acid molecules may be derived from one or more cells. Preparation of nucleic acid molecules may comprise generation of one or more mutations, such as strand-specific mutations. Nucleic acid molecules may be prepared for and analyzed by sequencing. Sequences may be identified with nucleic acid orientation information.

公开(公告)号：US20220033888A1

公开(公告)日：2022-02-03

申请号：US17312247

申请日：2019-12-06

Applicant: 10x Genomics, Inc.

Inventor： Michael Schnall-Levin ,  Eswar Prasad Ramachandran Iyer ,  Yifeng Yin ,  Tarjei Sigurd Mikkelsen ,  Preyas Shah ,  Geoffrey McDermott ,  Adam Lowe ,  Joshua Delaney ,  Augusto Manuel Tentori ,  Rajiv Bharadwaj ,  Stefania Giacomello ,  Alexander Gagnon ,  Meghan L. F. Frey ,  Zachary Bent ,  Erik Leonard Henrik Borgstrom

IPC: C12Q1/6837 ,  C12Q1/6881

Abstract: The present disclosure relates to compositions and methods for generating capture probes on a substrate for identifying the location of analytes in a biological sample.

公开(公告)号：US20220025446A1

公开(公告)日：2022-01-27

申请号：US17312069

申请日：2019-12-06

Applicant: 10x Genomics, Inc.

Inventor： Preyas Shah

IPC: C12Q1/6837 ,  C12Q1/6841

Abstract: This disclosure provides methods for spatial profiling of biological analytes present in a biological sample. Methods include generating feature arrays using a master/copy format using recessed arrays, and methods for using such arrays. For example spatially-tagged analyte capture analytes can be used in spatial detection in methods to determine the location of analytes (e.g., proteins) in biological samples.

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.