JP7579817B2 - Crisprで導入された二本鎖dna切断修復の同定、特徴付けおよび定量化 - Google Patents

Crisprで導入された二本鎖dna切断修復の同定、特徴付けおよび定量化 Download PDF

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JP7579817B2
JP7579817B2 JP2021577412A JP2021577412A JP7579817B2 JP 7579817 B2 JP7579817 B2 JP 7579817B2 JP 2021577412 A JP2021577412 A JP 2021577412A JP 2021577412 A JP2021577412 A JP 2021577412A JP 7579817 B2 JP7579817 B2 JP 7579817B2
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リー,ヘン
クルガン,ギャビン
マクニール,マシュー
ワン,ユー
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インテグレーティッド ディーエヌエイ テクノロジーズ インコーポレーティッド
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JP2021577412A 2019-07-03 2020-07-02 Crisprで導入された二本鎖dna切断修復の同定、特徴付けおよび定量化 Active JP7579817B2 (ja)

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US201962870471P 2019-07-03 2019-07-03
US201962870426P 2019-07-03 2019-07-03
US62/870,426 2019-07-03
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US201962952603P 2019-12-23 2019-12-23
US201962952598P 2019-12-23 2019-12-23
US62/952,598 2019-12-23
US62/952,603 2019-12-23
PCT/US2020/040621 WO2021003343A1 (en) 2019-07-03 2020-07-02 Identification, characterization, and quantitation of crispr-introduced double-stranded dna break repairs

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Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN119193713A (zh) 2019-10-24 2024-12-27 合成Dna技术公司 修饰的双链供体模板
CN119343462A (zh) 2022-05-13 2025-01-21 合成Dna技术公司 使用独特分子标识符改善长读测序的准确性和crispr编辑的表征
WO2026039499A1 (en) 2024-08-14 2026-02-19 Integrated Dna Technologies, Inc. Adaptered-tag blocking oligonucleotides

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20170053062A1 (en) 2014-01-27 2017-02-23 Georgia Tech Research Corporation Methods and systems for identifying crispr/cas off-target sites
US20170211142A1 (en) 2015-10-22 2017-07-27 The Broad Institute, Inc. Novel crispr enzymes and systems
US20180068062A1 (en) 2016-08-17 2018-03-08 The Broad Institute, Inc. Methods for identifying novel gene editing elements
US20180163265A1 (en) 2014-12-19 2018-06-14 The Broad Institute Inc. Unbiased identification of double-strand breaks and genomic rearrangement by genome-wide insert capture sequencing
JP2018518183A (ja) 2015-06-18 2018-07-12 ザ・ブロード・インスティテュート・インコーポレイテッド 新規crispr酵素及び系
JP2019504646A (ja) 2016-02-11 2019-02-21 ホライズン・ディスカバリー・リミテッド 複製的トランスポゾン系

Family Cites Families (23)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9809904B2 (en) 2011-04-21 2017-11-07 University Of Washington Through Its Center For Commercialization Methods for retrieval of sequence-verified DNA constructs
CN111254500B (zh) 2012-12-10 2024-01-23 分析生物科学有限公司 靶向基因组分析的方法
CA2906365A1 (en) 2013-03-15 2014-09-18 Integrated Dna Technologies, Inc. Rnase h-based assays utilizing modified rna monomers
US11306328B2 (en) 2013-07-26 2022-04-19 President And Fellows Of Harvard College Genome engineering
CN106604994B (zh) 2014-06-23 2021-12-14 通用医疗公司 通过测序评估的DSBs的全基因组无偏鉴定(GUIDE-Seq)
WO2016030899A1 (en) 2014-08-28 2016-03-03 Yeda Research And Development Co. Ltd. Methods of treating amyotrophic lateral scleroses
EP3221813A4 (en) 2014-11-20 2018-04-18 Children's Medical Center Corporation Methods relating to the detection of recurrent and non-specific double strand breaks in the genome
WO2016138500A1 (en) 2015-02-27 2016-09-01 Cellular Research, Inc. Methods and compositions for barcoding nucleic acids for sequencing
JP2018523991A (ja) 2015-06-22 2018-08-30 マクマスター・ユニバーシティMcmaster University 構造スイッチングのタンデム反応、核酸分解消化および核酸アセンブリーの増幅を含むバイオセンサー
WO2017040511A1 (en) 2015-08-31 2017-03-09 Agilent Technologies, Inc. Compounds and methods for crispr/cas-based genome editing by homologous recombination
US20170081679A1 (en) 2015-09-22 2017-03-23 Jie Xu Methods of improving nuclease mediated homologous recombination
EP4144844B1 (en) 2015-10-12 2025-09-10 DuPont US Holding, LLC Protected dna templates for gene modification and increased homologous recombination in cells and methods of use
CN116064748A (zh) 2015-11-25 2023-05-05 综合基因技术公司 用于变体检测的方法
ES2962711T3 (es) 2016-12-20 2024-03-20 Bristol Myers Squibb Co Métodos para aumentar la eficacia de la reparación dirigida por homología (HDR) en el genoma celular
US11981898B2 (en) 2017-06-16 2024-05-14 Applied Stemcell, Inc. Gene editing methods with increased knock-in efficiency
US20190062736A1 (en) * 2017-08-22 2019-02-28 Board Of Regents, The University Of Texas System In situ and in vivo analysis of chromatin interactions by biotinylated dcas9 protein
EP3679143A1 (en) 2017-09-08 2020-07-15 Life Technologies Corporation Methods for improved homologous recombination and compositions thereof
WO2019110067A1 (en) 2017-12-07 2019-06-13 Aarhus Universitet Hybrid nanoparticle
US12406749B2 (en) * 2017-12-15 2025-09-02 The Broad Institute, Inc. Systems and methods for predicting repair outcomes in genetic engineering
BR112020018902A2 (pt) 2018-03-20 2021-01-26 Tokyo Institute Of Technology oligonucleotídeo antissenso com toxicidade reduzida
WO2019246553A1 (en) * 2018-06-21 2019-12-26 Memorial Sloan Kettering Cancer Center Compositions & methods for monitoring dna repair
EP3935185A1 (en) 2019-03-04 2022-01-12 King Abdullah University Of Science And Technology Compositions and methods of labeling nucleic acids and sequencing and analysis thereof
CN119193713A (zh) 2019-10-24 2024-12-27 合成Dna技术公司 修饰的双链供体模板

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20170053062A1 (en) 2014-01-27 2017-02-23 Georgia Tech Research Corporation Methods and systems for identifying crispr/cas off-target sites
US20180163265A1 (en) 2014-12-19 2018-06-14 The Broad Institute Inc. Unbiased identification of double-strand breaks and genomic rearrangement by genome-wide insert capture sequencing
JP2018518183A (ja) 2015-06-18 2018-07-12 ザ・ブロード・インスティテュート・インコーポレイテッド 新規crispr酵素及び系
US20170211142A1 (en) 2015-10-22 2017-07-27 The Broad Institute, Inc. Novel crispr enzymes and systems
JP2019504646A (ja) 2016-02-11 2019-02-21 ホライズン・ディスカバリー・リミテッド 複製的トランスポゾン系
US20180068062A1 (en) 2016-08-17 2018-03-08 The Broad Institute, Inc. Methods for identifying novel gene editing elements

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WO2021003343A1 (en) 2021-01-07
CA3144106A1 (en) 2021-01-07
AU2020301025A1 (en) 2022-01-20
US20250218536A1 (en) 2025-07-03
JP2022540792A (ja) 2022-09-20
US12254959B2 (en) 2025-03-18
JP2025014002A (ja) 2025-01-28
EP3994258A1 (en) 2022-05-11
US20210002700A1 (en) 2021-01-07
IL289421A (en) 2022-02-01

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