公开(公告)号：US11046995B2

公开(公告)日：2021-06-29

申请号：US16315975

申请日：2017-08-14

Applicant: The Regents of the University of California

Inventor： Emily D. Crawford ,  Eric D. Chow ,  Joseph L. DeRisi

IPC: C12Q1/6806 ,  C12N15/10 ,  C12N9/22 ,  C12N15/11 ,  C12Q1/6855 ,  C12Q1/6869

Abstract: A method of sample analysis is provided. In some embodiments, the method comprises: (a) digesting a mixed nucleic acid sample with a plurality of reprogrammed nucleic acid-directed endonucleases that target sequences of interest to produce a digested sample, wherein at least some of the fragments in the digested sample comprise: (i) a sequence of interest and (ii) at least one ligatable end that has been generated by endonuclease cleavage; (b) enriching for fragments that contain the sequence of interest; and (c) analyzing the enriched fragments. Kits for performing the method are also provided.

公开(公告)号：US20190300935A1

公开(公告)日：2019-10-03

申请号：US16315975

申请日：2017-08-14

Applicant: The Regents of the University of California

Inventor： Emily D. Crawford ,  Eric D. Chow ,  Joseph L. DeRisi

IPC: C12Q1/6806 ,  C12N9/22 ,  C12N15/11 ,  C12Q1/6855 ,  C12Q1/6869

Abstract: A method of sample analysis is provided. In some embodiments, the method comprises: (a) digesting a mixed nucleic acid sample with a plurality of reprogrammed nucleic acid-directed endonucleases that target sequences of interest to produce a digested sample, wherein at least some of the fragments in the digested sample comprise: (i) a sequence of interest and (ii) at least one ligatable end that has been generated by endonuclease cleavage; (b) enriching for fragments that contain the sequence of interest; and (c) analyzing the enriched fragments. Kits for performing the method are also provided.

公开(公告)号：US20180051320A1

公开(公告)日：2018-02-22

申请号：US15348855

申请日：2016-11-10

Applicant: The Regents of the University of California

Inventor： Joseph L. DeRisi ,  Wei Gu ,  Emily D. Crawford ,  Brian O'Donovan ,  Michael Wilson ,  Eric D. Chow ,  Hanna Retallack

IPC: C12Q1/68

CPC classification number: C12Q1/6806 ,  C12Q1/6848 ,  C12Q1/6874 ,  C12Q2521/301

Abstract: Among other things, this disclosure describes a method comprising: cleaving a plurality of target sequences in an adaptor-tagged sequencing library using population of reprogrammed nucleic acid-directed endonucleases; non-specifically amplifying the library, thereby amplifying fragments that have not been cleaved; and sequencing the amplified sample.

公开(公告)号：US20250034554A1

公开(公告)日：2025-01-30

申请号：US18782679

申请日：2024-07-24

Applicant: The Regents of the University of California

Inventor： Amy Yi-Tyng Chang ,  Eric D. Chow ,  Brandon Kwan-Leong

IPC: C12N15/10 ,  C12M1/12 ,  C12M1/30 ,  C12M1/36 ,  C40B60/00 ,  G01N35/00 ,  G01N35/10

Abstract: Provided are methods and compositions for creating an arrayed library of cells. In particular, the methods and compositions provided herein improve the selection and transfer of cells by reducing contamination, increasing throughput, and improving consistency of transfer. Such methods and compositions include automated colony selection employing a solid barrier mounted on an automated apparatus for automatic handling of one or more pick tools. The solid barrier is configured to prevent undesired transfer of cells from a pick tool into the destination receptacle. Such methods and compositions also include acoustic transfer of cells in a high-density media by an acoustic liquid handler. The methods and compositions further include pooling the cells using a bitcode sample pooling scheme for high-throughput sequencing and deconvoluting the obtained nucleic acid sequences to identify the cells from which the sequences originated.

公开(公告)号：US12077826B2

公开(公告)日：2024-09-03

申请号：US17258420

申请日：2019-07-08

Applicant: The Regents of The University of California

Inventor： Zev J. Gartner ,  David Patterson ,  Eric D. Chow ,  Robert Weber ,  Christopher McGinnis

IPC: C12Q1/6886 ,  C12Q1/6806

CPC classification number: C12Q1/6886 ,  C12Q1/6806 ,  C12Q2600/158

Abstract: Disclosed are compositions comprising a first lipid-conjugated oligonucleotide comprising a first lipid moiety, a first hybridization region, and a first primer region; a second lipid-conjugated oligonucleotide comprising a second hybridization region and a second lipid moiety, wherein the second hybridization region is the reverse complement of the first hybridization region; and a third oligonucleotide comprising a second primer region, a barcode region, and a capture sequence, wherein the second primer region is the reverse complement of the first primer region; compositions comprising a lipid-conjugated DNA oligonucleotide comprising a lipid moiety, a barcode region, and a capture sequence; and composition comprising a first lipid-conjugated DNA oligonucleotide comprising a lipid moiety and a first primer region; and a second DNA oligonucleotide comprising a second primer region, a barcode region, and a capture sequence, wherein the second primer region is the reverse complement of the first primer region. Also disclosed are membranes and cells comprising such compositions and uses of such compositions.

公开(公告)号：US20210388447A1

公开(公告)日：2021-12-16

申请号：US17258420

申请日：2019-07-08

Applicant: The Regents of The University of California

Inventor： Zev J. Gartner ,  David Patterson ,  Eric D. Chow ,  Robert Weber ,  Christopher McGinnis

IPC: C12Q1/6886 ,  C12Q1/6806

Abstract: Disclosed are compositions comprising a first lipid-conjugated oligonucleotide comprising a first lipid moiety, a first hybridization region, and a first primer region; a second lipid-conjugated oligonucleotide comprising a second hybridization region and a second lipid moiety, wherein the second hybridization region is the reverse complement of the first hybridization region; and a third oligonucleotide comprising a second primer region, a barcode region, and a capture sequence, wherein the second primer region is the reverse complement of the first primer region; compositions comprising a lipid-conjugated DNA oligonucleotide comprising a lipid moiety, a barcode region, and a capture sequence; and composition comprising a first lipid-conjugated DNA oligonucleotide comprising a lipid moiety and a first primer region; and a second DNA oligonucleotide comprising a second primer region, a barcode region, and a capture sequence, wherein the second primer region is the reverse complement of the first primer region. Also disclosed are membranes and cells comprising such compositions and uses of such compositions.