Additional file 2: of Guide RNAs with embedded barcodes boost CRISPR-pooled screens

Additional file 1: of Viral diversity is an obligate consideration in CRISPR/Cas9 designs for targeting the HIV reservoir

Pavitra Roychoudhury (4720350)
Harshana De Silva Feelixge (5506538)
Daniel Reeves (4720356)
Bryan Mayer (5506541)
Daniel Stone (186682)
Joshua Schiffer (4720353)
Keith Jerome (4978262)

July 2018

Table S1. (A) Correlation between predicted activity and target site conservation. (B) Correlation b...

Additional file 1: of Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

Francesco Iorio (408438)
Fiona Behan (5626649)
Emanuel Gonรงalves (5626652)
Shriram Bhosle (10114)
Elisabeth Chen (5626655)
Rebecca Shepherd (5626658)
Charlotte Beaver (5626661)
Rizwan Ansari (5626667)
Rachel Pooley (5626670)
Piers Wilkinson (5626673)
Sarah Harper (5226377)
Adam Butler (658177)
Euan Stronach (5626676)
Julio Saez-Rodriguez (25229)
Kosuke Yusa (3175638)
Mathew Garnett (408439)

August 2018

Table S1. Project Score cell lines included in the study with annotations and screening description....

Additional file 7: of iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity

Christopher Nobles (6241982)
Shantan Reddy (6241985)
January Salas-McKee (6241988)
Xiaojun Liu (58952)
Carl June (6241991)
J. Melenhorst (6241994)
Megan Davis (6241997)
Yangbing Zhao (6242000)
Frederic Bushman (3286380)

January 2019

Figure S2. Human genome sequences with near matches to the B2M, TRAC5, and VEGFA sgRNAs, with data o...

Additional file 3: of Guide RNAs with embedded barcodes boost CRISPR-pooled screens

Shiyou Zhu (464020)
Zhongzheng Cao (6262205)
Zhiheng Liu (341545)
Yuan He (82781)
Yinan Wang (478812)
Pengfei Yuan (464019)
Wei Li (7081)
Feng Tian (121350)
Ying Bao (267477)
Wensheng Wei (464022)

January 2019

Table S4. Results of the human genome-scale sgRNAiBAR library screening at different MOI for the cyt...

Additional file 1: of Guide RNAs with embedded barcodes boost CRISPR-pooled screens

Shiyou Zhu (464020)
Zhongzheng Cao (6262205)
Zhiheng Liu (341545)
Yuan He (82781)
Yinan Wang (478812)
Pengfei Yuan (464019)
Wei Li (7081)
Feng Tian (121350)
Ying Bao (267477)
Wensheng Wei (464022)

January 2019

Figure S1. CRISPR screening of a collection of sgRNAsiBAR-ANTXR1 containing all 4096 types of iBAR6 ...

Additional file 2: of Development of drug-inducible CRISPR-Cas9 systems for large-scale functional screening

Ning Sun (162468)
Sakina Petiwala (6486374)
Rui Wang (52434)
Charles Lu (33589)
Mufeng Hu (6486377)
Sujana Ghosh (6486380)
Yan Hao (113600)
Christopher Miller (1120)
Namjin Chung (413823)

March 2019

Table S2. Raw NGS count table for FACS-based CRISPR screening using constitutive sgRNA expression ve...

Additional file 2: of CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors

Haroon Butt (3864433)
Ayman Eid (777468)
Afaque Momin (6648473)
Jeremie Bazin (6648476)
Martin Crespi (231072)
Stefan Arold (487269)
Magdy Mahfouz (777477)

April 2019

Table S1. Sequences of sgRNAs with PAM targeting SF3B1. Table S2. List of primers annealed to synthe...

Additional file 1: of Pooled extracellular receptor-ligand interaction screening using CRISPR activation

Zheng-Shan Chong (6011456)
Shuhei Ohnishi (3225636)
Kosuke Yusa (3175638)
Gavin Wright (436365)

November 2018

Table S1. A table listing the gRNAs sequences targeting the promoter regions for the named genes. Th...

Additional file 2: Table S1. of Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening

Michael Kiessling (3480242)
Sven Schuierer (1933723)
Silke Stertz (367516)
Martin Beibel (3480251)
Sebastian Bergling (785781)
Judith Knehr (3480248)
Walter Carbone (3480254)
Cheryl de ValliĂ¨re (3480245)
Joelle Tchinda (3480239)
Tewis Bouwmeester (4352)
Klaus Seuwen (34678)
Gerhard Rogler (139954)
Guglielmo Roma (155263)

September 2016

Correlation of sgRNA library distribution between technical replicates in HCC-827 and CHP-212 cells....

Additional file 3: Table S2. of Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening

Michael Kiessling (3480242)
Sven Schuierer (1933723)
Silke Stertz (367516)
Martin Beibel (3480251)
Sebastian Bergling (785781)
Judith Knehr (3480248)
Walter Carbone (3480254)
Cheryl de ValliĂ¨re (3480245)
Joelle Tchinda (3480239)
Tewis Bouwmeester (4352)
Klaus Seuwen (34678)
Gerhard Rogler (139954)
Guglielmo Roma (155263)

September 2016

Correlation of sgRNA library distribution between technical replicates of HCC-827 and CHP-212 cells....

Additional file 1: Table S1. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

Maximilian Haeussler (86348)
Kai Schönig (261411)
Hélène Eckert (3577886)
Alexis Eschstruth (535535)
Joffrey Mianné (3407417)
Jean-Baptiste Renaud (230969)
Sylvie Schneider-Maunoury (2557627)
Alena Shkumatava (3577880)
Lydia Teboul (106309)
Jim Kent (274755)
Jean-Stephane Joly (3577883)
Jean-Paul Concordet (269984)

July 2016

Detailed information about CRISPR/Cas9 off-target studies, including first author, PMID, name of the...

Additional file 2: Table S2. of CRISPR/Cas9-mediated targeted chromosome elimination

Erwei Zuo (4682140)
Xiaona Huo (4682134)
Xuan Yao (344579)
Xinde Hu (4682137)
Yidi Sun (148763)
Jianhang Yin (4682122)
Bingbing He (4682125)
Xing Wang (154377)
Linyu Shi (4682119)
Jie Ping (137209)
Yu Wei (365236)
Wenqin Ying (4682131)
Wei Wei (21173)
Wenjia Liu (118146)
Cheng Tang (439042)
Yixue Li (18673)
Jiazhi Hu (4682128)
Hui Yang (91136)

November 2017

Unique and multiple repeated sequences for targeting by a single specific sgRNA. (XLSX 9524 kb

Additional file 3: of Pooled extracellular receptor-ligand interaction screening using CRISPR activation

Zheng-Shan Chong (6011456)
Shuhei Ohnishi (3225636)
Kosuke Yusa (3175638)
Gavin Wright (436365)

November 2018

A table detailing all the gRNA sequences present in the CRISPRa library. For each named gene, the gR...

Additional file 1: Figure S1. of Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool

Jihyeob Mun (3602387)
Dong-Uk Kim (77753)
Kwang-Lae Hoe (51453)
Seon-Young Kim (91302)

December 2016

Pipelines of pooled library screen analysis. Table S1. Public library sets of shRNA, sgRNA and delet...

Additional file 4: of Enhanced mammalian genome editing by new Cas12a orthologs with optimized crRNA scaffolds

Fei Teng (201085)
Jing Li (10611)
Tongtong Cui (6296321)
Kai Xu (122914)
Lu Guo (281252)
Qingqin Gao (6296324)
Guihai Feng (226799)
Chuanyuan Chen (6296333)
Dali Han (1468663)
Qi Zhou (7408)
Wei Li (7081)

February 2019

Table S2. Sequences of targeting crRNAs used for in vitro RNA transcription. Table S3. Target sequen...

Additional file 1: of Viral diversity is an obligate consideration in CRISPR/Cas9 designs for targeting the HIV reservoir

Pavitra Roychoudhury (4720350)
Harshana De Silva Feelixge (5506538)
Daniel Reeves (4720356)
Bryan Mayer (5506541)
Daniel Stone (186682)
Joshua Schiffer (4720353)
Keith Jerome (4978262)

July 2018

Table S1. (A) Correlation between predicted activity and target site conservation. (B) Correlation b...

Additional file 1: of Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

Francesco Iorio (408438)
Fiona Behan (5626649)
Emanuel Gonรงalves (5626652)
Shriram Bhosle (10114)
Elisabeth Chen (5626655)
Rebecca Shepherd (5626658)
Charlotte Beaver (5626661)
Rizwan Ansari (5626667)
Rachel Pooley (5626670)
Piers Wilkinson (5626673)
Sarah Harper (5226377)
Adam Butler (658177)
Euan Stronach (5626676)
Julio Saez-Rodriguez (25229)
Kosuke Yusa (3175638)
Mathew Garnett (408439)

August 2018

Table S1. Project Score cell lines included in the study with annotations and screening description....

Additional file 7: of iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity

Christopher Nobles (6241982)
Shantan Reddy (6241985)
January Salas-McKee (6241988)
Xiaojun Liu (58952)
Carl June (6241991)
J. Melenhorst (6241994)
Megan Davis (6241997)
Yangbing Zhao (6242000)
Frederic Bushman (3286380)

January 2019

Figure S2. Human genome sequences with near matches to the B2M, TRAC5, and VEGFA sgRNAs, with data o...

Additional file 3: of Guide RNAs with embedded barcodes boost CRISPR-pooled screens

Shiyou Zhu (464020)
Zhongzheng Cao (6262205)
Zhiheng Liu (341545)
Yuan He (82781)
Yinan Wang (478812)
Pengfei Yuan (464019)
Wei Li (7081)
Feng Tian (121350)
Ying Bao (267477)
Wensheng Wei (464022)

January 2019

Table S4. Results of the human genome-scale sgRNAiBAR library screening at different MOI for the cyt...

Additional file 1: of Guide RNAs with embedded barcodes boost CRISPR-pooled screens

Shiyou Zhu (464020)
Zhongzheng Cao (6262205)
Zhiheng Liu (341545)
Yuan He (82781)
Yinan Wang (478812)
Pengfei Yuan (464019)
Wei Li (7081)
Feng Tian (121350)
Ying Bao (267477)
Wensheng Wei (464022)

January 2019

Figure S1. CRISPR screening of a collection of sgRNAsiBAR-ANTXR1 containing all 4096 types of iBAR6 ...

Additional file 2: of Development of drug-inducible CRISPR-Cas9 systems for large-scale functional screening

Ning Sun (162468)
Sakina Petiwala (6486374)
Rui Wang (52434)
Charles Lu (33589)
Mufeng Hu (6486377)
Sujana Ghosh (6486380)
Yan Hao (113600)
Christopher Miller (1120)
Namjin Chung (413823)

March 2019

Table S2. Raw NGS count table for FACS-based CRISPR screening using constitutive sgRNA expression ve...

Additional file 2: of CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors

Haroon Butt (3864433)
Ayman Eid (777468)
Afaque Momin (6648473)
Jeremie Bazin (6648476)
Martin Crespi (231072)
Stefan Arold (487269)
Magdy Mahfouz (777477)

April 2019

Table S1. Sequences of sgRNAs with PAM targeting SF3B1. Table S2. List of primers annealed to synthe...

Additional file 1: of Pooled extracellular receptor-ligand interaction screening using CRISPR activation

Zheng-Shan Chong (6011456)
Shuhei Ohnishi (3225636)
Kosuke Yusa (3175638)
Gavin Wright (436365)

November 2018

Table S1. A table listing the gRNAs sequences targeting the promoter regions for the named genes. Th...

Additional file 2: Table S1. of Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening

Michael Kiessling (3480242)
Sven Schuierer (1933723)
Silke Stertz (367516)
Martin Beibel (3480251)
Sebastian Bergling (785781)
Judith Knehr (3480248)
Walter Carbone (3480254)
Cheryl de ValliĂ¨re (3480245)
Joelle Tchinda (3480239)
Tewis Bouwmeester (4352)
Klaus Seuwen (34678)
Gerhard Rogler (139954)
Guglielmo Roma (155263)

September 2016

Correlation of sgRNA library distribution between technical replicates in HCC-827 and CHP-212 cells....

Additional file 3: Table S2. of Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening

Michael Kiessling (3480242)
Sven Schuierer (1933723)
Silke Stertz (367516)
Martin Beibel (3480251)
Sebastian Bergling (785781)
Judith Knehr (3480248)
Walter Carbone (3480254)
Cheryl de ValliĂ¨re (3480245)
Joelle Tchinda (3480239)
Tewis Bouwmeester (4352)
Klaus Seuwen (34678)
Gerhard Rogler (139954)
Guglielmo Roma (155263)

September 2016

Correlation of sgRNA library distribution between technical replicates of HCC-827 and CHP-212 cells....

Additional file 1: Table S1. of Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

Maximilian Haeussler (86348)
Kai Schönig (261411)
Hélène Eckert (3577886)
Alexis Eschstruth (535535)
Joffrey Mianné (3407417)
Jean-Baptiste Renaud (230969)
Sylvie Schneider-Maunoury (2557627)
Alena Shkumatava (3577880)
Lydia Teboul (106309)
Jim Kent (274755)
Jean-Stephane Joly (3577883)
Jean-Paul Concordet (269984)

July 2016

Detailed information about CRISPR/Cas9 off-target studies, including first author, PMID, name of the...

Additional file 2: Table S2. of CRISPR/Cas9-mediated targeted chromosome elimination

Erwei Zuo (4682140)
Xiaona Huo (4682134)
Xuan Yao (344579)
Xinde Hu (4682137)
Yidi Sun (148763)
Jianhang Yin (4682122)
Bingbing He (4682125)
Xing Wang (154377)
Linyu Shi (4682119)
Jie Ping (137209)
Yu Wei (365236)
Wenqin Ying (4682131)
Wei Wei (21173)
Wenjia Liu (118146)
Cheng Tang (439042)
Yixue Li (18673)
Jiazhi Hu (4682128)
Hui Yang (91136)

November 2017

Unique and multiple repeated sequences for targeting by a single specific sgRNA. (XLSX 9524 kb

Additional file 3: of Pooled extracellular receptor-ligand interaction screening using CRISPR activation

Zheng-Shan Chong (6011456)
Shuhei Ohnishi (3225636)
Kosuke Yusa (3175638)
Gavin Wright (436365)

November 2018

A table detailing all the gRNA sequences present in the CRISPRa library. For each named gene, the gR...

Additional file 1: Figure S1. of Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool

Jihyeob Mun (3602387)
Dong-Uk Kim (77753)
Kwang-Lae Hoe (51453)
Seon-Young Kim (91302)

December 2016

Pipelines of pooled library screen analysis. Table S1. Public library sets of shRNA, sgRNA and delet...

Additional file 4: of Enhanced mammalian genome editing by new Cas12a orthologs with optimized crRNA scaffolds

Fei Teng (201085)
Jing Li (10611)
Tongtong Cui (6296321)
Kai Xu (122914)
Lu Guo (281252)
Qingqin Gao (6296324)
Guihai Feng (226799)
Chuanyuan Chen (6296333)
Dali Han (1468663)
Qi Zhou (7408)
Wei Li (7081)

February 2019

Table S2. Sequences of targeting crRNAs used for in vitro RNA transcription. Table S3. Target sequen...

Additional file 1: of Viral diversity is an obligate consideration in CRISPR/Cas9 designs for targeting the HIV reservoir

Pavitra Roychoudhury (4720350)
Harshana De Silva Feelixge (5506538)
Daniel Reeves (4720356)
Bryan Mayer (5506541)
Daniel Stone (186682)
Joshua Schiffer (4720353)
Keith Jerome (4978262)

July 2018

Table S1. (A) Correlation between predicted activity and target site conservation. (B) Correlation b...

Additional file 1: of Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

Francesco Iorio (408438)
Fiona Behan (5626649)
Emanuel Gonรงalves (5626652)
Shriram Bhosle (10114)
Elisabeth Chen (5626655)
Rebecca Shepherd (5626658)
Charlotte Beaver (5626661)
Rizwan Ansari (5626667)
Rachel Pooley (5626670)
Piers Wilkinson (5626673)
Sarah Harper (5226377)
Adam Butler (658177)
Euan Stronach (5626676)
Julio Saez-Rodriguez (25229)
Kosuke Yusa (3175638)
Mathew Garnett (408439)

August 2018

Table S1. Project Score cell lines included in the study with annotations and screening description....

Additional file 7: of iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity

Christopher Nobles (6241982)
Shantan Reddy (6241985)
January Salas-McKee (6241988)
Xiaojun Liu (58952)
Carl June (6241991)
J. Melenhorst (6241994)
Megan Davis (6241997)
Yangbing Zhao (6242000)
Frederic Bushman (3286380)

January 2019

Figure S2. Human genome sequences with near matches to the B2M, TRAC5, and VEGFA sgRNAs, with data o...

Additional file 2: of Guide RNAs with embedded barcodes boost CRISPR-pooled screens

Abstract

Extracted data

Additional file 2: of Guide RNAs with embedded barcodes boost CRISPR-pooled screens

Abstract

Extracted data

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