公开(公告)号：US20240060127A1

公开(公告)日：2024-02-22

申请号：US18343108

申请日：2023-06-28

Applicant: 10x Genomics, Inc.

Inventor： Denis PRISTINSKI ,  Preyas SHAH ,  Siyuan XING

IPC: C12Q1/6874 ,  C12Q1/6876 ,  G03F7/00

CPC classification number: C12Q1/6874 ,  C12Q1/6876 ,  G03F7/0035

Abstract: Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate using a minimal mask scheme. Systems and kits employing the methods are also disclosed. In some embodiments, a method disclosed herein comprises using photomasks and photoresist for photocontrollable hybridization and/or ligation of nucleic acid molecules, wherein photoresist removal allows hybridization and/or ligation of nucleic acid molecules at the exposed area. A large diversity of barcodes can be created in molecules on the substrate via sequential rounds of light exposure, hybridization, and ligation.

公开(公告)号：US20240076721A1

公开(公告)日：2024-03-07

申请号：US18342948

申请日：2023-06-28

Applicant: 10x Genomics, Inc.

Inventor： Preyas SHAH

IPC: C12Q1/6834

CPC classification number: C12Q1/6834

Abstract: The present disclosure relates in some aspects to methods for manufacturing molecular arrays using a hybrid approach comprising microfluidics-based delivery and photolithography-guided oligonucleotide hybridization and ligation. In particular, the molecular arrays can be used for determining spatial patterns of abundance and/or expression of a biological target in a sample.

公开(公告)号：US20240084359A1

公开(公告)日：2024-03-14

申请号：US18342891

申请日：2023-06-28

Applicant: 10x Genomics, Inc.

Inventor： Michael SCHNALL-LEVIN ,  Preyas SHAH

IPC: C12Q1/6806 ,  B01L3/00 ,  C12Q1/6874 ,  C12Q1/6888

CPC classification number: C12Q1/6806 ,  B01L3/50857 ,  C12Q1/6874 ,  C12Q1/6888 ,  B01L2300/0829

Abstract: Provided in some aspects are methods of patterning a surface in situ for producing an array on the surface, for example, by partitioning of beads comprising oligonucleotides into spatially predefined regions, to generate unique DNA sequences in spatial positions in the array. Compositions such as nucleic acid arrays produced by the methods are also disclosed.

公开(公告)号：US20220228210A1

公开(公告)日：2022-07-21

申请号：US17565047

申请日：2021-12-29

Applicant: 10x Genomics, Inc.

Inventor： David Michael PATTERSON ,  Denis PRISTINSKI ,  Preyas SHAH ,  Steven William SHORT ,  Dieter WILK ,  Siyuan XING

IPC: C12Q1/6874 ,  C12N15/10

Abstract: Provided in some aspects are methods for light-controlled in situ surface patterning of a substrate. Compositions such as nucleic acid arrays produced by the methods are also disclosed. In some embodiments, a method disclosed herein comprises using photoresist for photocontrollable hybridization and/or ligation of nucleic acid molecules, wherein photoresist removal allows hybridization and/or ligation of nucleic acid molecules at the exposed area. A large diversity of barcodes can be created in molecules on the substrate via sequential rounds of light exposure, hybridization, and ligation.

公开(公告)号：US20210324465A1

公开(公告)日：2021-10-21

申请号：US17232017

申请日：2021-04-15

Applicant: 10x Genomics, Inc.

Inventor： Preyas SHAH ,  Li WANG ,  Brett OLSEN

IPC: C12Q1/6874 ,  C12Q1/6806

Abstract: A method for conducting a customized analysis of open chromatin regions on a cell, comprising receiving an output file for a cell barcode genomic sequence dataset, the output file comprising a peak-barcode matrix, wherein each peak is defined by a plurality of fragment sequences aligned within a peak region, a unique barcode is associated with each fragment sequence in the dataset, and the peak-barcode matrix pairs each peak with the barcodes of the aligned fragments; and cell clusters with cells aggregated based on similarity in accessibility of specific transcription factor binding motifs associated with each cell, wherein the accessibility is determined via a differential accessibility analysis. The method further comprises adjusting customizable parameters for analyzing the peak-barcode matrix, and generating an updated output file including an updated clustering of cells, based on the customizable parameters, wherein each updated cell cluster includes cells with peaks representing a specific gene regulatory function.

公开(公告)号：US20240428880A1

公开(公告)日：2024-12-26

申请号：US18827279

申请日：2024-09-06

Applicant: 10x Genomics, Inc.

Inventor： Patrick J. MARKS ,  Preyas SHAH

IPC: G16B15/00 ,  G16B25/20 ,  G16B50/50

Abstract: Methods and systems for performing in situ decoding are described that minimize optical crowding, thereby improving decoding accuracy. The methods may comprise, e.g., receiving images of a biological sample acquired during a cyclical decoding process; detecting a series of detectable signals (ON signals) or absence thereof (OFF signals) at one or more locations in the biological sample corresponding to one or more barcoded target analytes; determining a code word based on the series of ON and OFF signals that corresponds to a barcode for each of the one or more barcoded target analytes, where the one or more code words are assigned to the one or more barcoded target analytes based on a minimax decision rule to minimize a density of ON signals detected in the images of the series of images; and identifying the one or more barcoded target analytes based on the one or more determined code words.

公开(公告)号：US20220084629A1

公开(公告)日：2022-03-17

申请号：US17476395

申请日：2021-09-15

Applicant: 10x Genomics, Inc.

Inventor： Preyas SHAH

IPC: G16B30/10 ,  G16B30/20 ,  G16B15/00

Abstract: Methods and systems for designing large sets of barcodes that ensure robust and efficient error correction capabilities are described. Also described are methods for assigning barcodes to target analytes that minimize optical crowding in in situ detection applications. Furthermore, methods for performing barcode error correction and for performing barcode-assisted image registration and alignment are also described.

公开(公告)号：US20220084628A1

公开(公告)日：2022-03-17

申请号：US17476398

申请日：2021-09-15

Applicant: 10x Genomics, Inc.

Inventor： Preyas SHAH

IPC: G16B25/20 ,  G16B5/20 ,  G06K7/14

Abstract: Methods and systems for designing large sets of barcodes that ensure robust and efficient error correction capabilities are described. Also described are methods for assigning barcodes to target analytes that minimize optical crowding in in situ detection applications. Furthermore, methods for performing barcode error correction and for performing barcode-assisted image registration and alignment are also described.

公开(公告)号：US20220083832A1

公开(公告)日：2022-03-17

申请号：US17476400

申请日：2021-09-15

Applicant: 10x Genomics, Inc.

Inventor： Preyas SHAH

IPC: G06K19/06 ,  G16B30/20 ,  G16B30/10

Abstract: Methods and systems for designing large sets of barcodes that ensure robust and efficient error correction capabilities are described. Also described are methods for assigning barcodes to target analytes that minimize optical crowding in in situ detection applications. Furthermore, methods for performing barcode error correction and for performing barcode-assisted image registration and alignment are also described.