Additional file 1: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Additional file 1 of Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Xin Fang (134979)
Jonathan Monk (3548066)
Nathan Mih (3146436)
Bin Du (138774)
Anand Sastry (5369741)
Erol Kavvas (3465563)
Yara Seif (4908814)
Larry Smarr (379158)
Bernhard Palsson (450761)

June 2018

Table S1: Metadata of 110 strains. Table S2: Genes associated with mucus degradation. Table S3: Meta...

Additional file 3: of Enrichment of in vivo transcription data from dietary intervention studies with in vitro data provides improved insight into gene regulation mechanisms in the intestinal mucosa

Marcel Hulst (3122097)
Alfons Jansman (3849133)
Ilonka Wijers (3923252)
Arjan Hoekman (3122112)
StĂŠphanie Vastenhouw (3923261)
Marinus van Krimpen (3923249)
Mari Smits (3122115)
Dirkjan Schokker (579932)

April 2017

Table S3. Full names of overlapping DEGs expressed in vivo and in vitro ZnO, rye and amoxicillin int...

Additional file 7: of Comparative analysis of sequencing technologies for single-cell transcriptomics

Kedar Natarajan (3563123)
Zhichao Miao (838497)
Miaomiao Jiang (559714)
Xiaoyun Huang (659874)
Hongpo Zhou (6566438)
Jiarui Xie (6566441)
Chunqing Wang (3702286)
Shishang Qin (6566444)
Zhikun Zhao (6566447)
Liang Wu (131111)
Naibo Yang (3097908)
Bo Li (112195)
Yong Hou (420455)
Shiping Liu (79385)
Sarah Teichmann (3553601)

April 2019

Table S5. Single-cell library statistics computed from randomly downsampled 1 million paired-end seq...

Additional file 10: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Table S6. SeqWell reverse transcription and library preparation primers. (DOCX 13 kb

Additional file 7: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Figure S3. Quality metrics for single-cell RNA sequencing. A Total gene number of cells maintained i...

Additional file 4: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Figure S2. Proteomic pipeline, sample-to-sample comparison, and insights from the in vitro PC proteo...

Additional file 8: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Figure S4. Signaling pathways and processes associated with in vitro PC enrichment (Additional file ...

Additional file 22: Table S3. of Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment

Sweta Roy-Carson (3922934)
Kevin Natukunda (3922943)
Hsien-chao Chou (3922928)
Narinder Pal (3922937)
Caitlin Farris (3922931)
Stephan Schneider (503788)
Julie Kuhlman (3922940)

April 2017

List of molecular functions and their associated values for the present dataset. Table of all the va...

Additional file 8: of Biphasic modulation of insulin signaling enables highly efficient hematopoietic differentiation from human pluripotent stem cells

Fuyu Duan (3690385)
Rujin Huang (3690379)
Fengzhi Zhang (335439)
Yonglin Zhu (5567597)
Lin Wang (11986)
Xia Chen (299366)
Lufeng Bai (5567600)
Wei Guo (86150)
Sophia Chang (3690382)
Xiaoyu Hu (4159)
Jie Na (221422)

July 2018

Table S3. DEseq2 gene list of significantly differentially expressed genes in day 8 HSPCs and ECs (X...

Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Szucs, Matthew J
Ammendolia, Dustin A
MacMullan, Melanie A
Rakoff-Nahoum, Seth
Mead, Benjamin Elliott
Ordovas-Montanes, Jose Manuel
Braun, Alexandra Provost
Levy, Lauren
Saluja, Prerna Bhargava
Yin, Xiaolei
Hughes, Travis K.
Wadsworth, Marc Havens
Ahmad, Rushdy
Carr, Steven A
Langer, Robert S
Collins, James J.
Shalek, Alexander K
Karp, Jeffrey Michael

June 2018

Background Single-cell genomic methods now provide unprecedented resolution for cha...

Additional file 1: of Cell maps on the human genome

Christopher Cherniak (6492422)
Raul Rodriguez-Esteban (257885)

March 2019

Table S1. GeneCts per chromosome and cellular location. Gene entries include all subcellular targets...

Additional file 2: of Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis

Ji Dong (553653)
Yuqiong Hu (4963780)
Xiaoying Fan (3419693)
Xinglong Wu (1347408)
Yunuo Mao (4963774)
Boqiang Hu (3419696)
Hongshan Guo (4963777)
Lu Wen (385160)
Fuchou Tang (14392)

March 2018

Barcode-RT primer information, cell cycle gene list, and E-, M- and S-score gene list. (XLSX 18 kb

Additional file 3: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Figure S1. Image analysis of cell clusters and flow cytometry. A Bright-field microscopy after 6 day...

Additional file 1: of Highly efficient and expedited hepatic differentiation from human pluripotent stem cells by pure small-molecule cocktails

Cong Du (2702083)
Yuan Feng (213823)
Dongbo Qiu (4927330)
Yan Xu (14594)
Mao Pang (710425)
Nan Cai (4927327)
Andy Xiang (3471293)
Qi Zhang (28502)

March 2018

Table S1. Small molecules used for hepatic differentiation. Table S2. Primers used to amplify the tr...

Additional file 1: of Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis

Ji Dong (553653)
Yuqiong Hu (4963780)
Xiaoying Fan (3419693)
Xinglong Wu (1347408)
Yunuo Mao (4963774)
Boqiang Hu (3419696)
Hongshan Guo (4963777)
Lu Wen (385160)
Fuchou Tang (14392)

March 2018

Figure S1. Quality control of the dataset and the characteristics of clusters. Figure S2. Interactio...

Additional file 1 of Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Xin Fang (134979)
Jonathan Monk (3548066)
Nathan Mih (3146436)
Bin Du (138774)
Anand Sastry (5369741)
Erol Kavvas (3465563)
Yara Seif (4908814)
Larry Smarr (379158)
Bernhard Palsson (450761)

June 2018

Table S1: Metadata of 110 strains. Table S2: Genes associated with mucus degradation. Table S3: Meta...

Additional file 3: of Enrichment of in vivo transcription data from dietary intervention studies with in vitro data provides improved insight into gene regulation mechanisms in the intestinal mucosa

Marcel Hulst (3122097)
Alfons Jansman (3849133)
Ilonka Wijers (3923252)
Arjan Hoekman (3122112)
StĂŠphanie Vastenhouw (3923261)
Marinus van Krimpen (3923249)
Mari Smits (3122115)
Dirkjan Schokker (579932)

April 2017

Table S3. Full names of overlapping DEGs expressed in vivo and in vitro ZnO, rye and amoxicillin int...

Additional file 7: of Comparative analysis of sequencing technologies for single-cell transcriptomics

Kedar Natarajan (3563123)
Zhichao Miao (838497)
Miaomiao Jiang (559714)
Xiaoyun Huang (659874)
Hongpo Zhou (6566438)
Jiarui Xie (6566441)
Chunqing Wang (3702286)
Shishang Qin (6566444)
Zhikun Zhao (6566447)
Liang Wu (131111)
Naibo Yang (3097908)
Bo Li (112195)
Yong Hou (420455)
Shiping Liu (79385)
Sarah Teichmann (3553601)

April 2019

Table S5. Single-cell library statistics computed from randomly downsampled 1 million paired-end seq...

Additional file 10: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Table S6. SeqWell reverse transcription and library preparation primers. (DOCX 13 kb

Additional file 7: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Figure S3. Quality metrics for single-cell RNA sequencing. A Total gene number of cells maintained i...

Additional file 4: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Figure S2. Proteomic pipeline, sample-to-sample comparison, and insights from the in vitro PC proteo...

Additional file 8: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Figure S4. Signaling pathways and processes associated with in vitro PC enrichment (Additional file ...

Additional file 22: Table S3. of Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment

Sweta Roy-Carson (3922934)
Kevin Natukunda (3922943)
Hsien-chao Chou (3922928)
Narinder Pal (3922937)
Caitlin Farris (3922931)
Stephan Schneider (503788)
Julie Kuhlman (3922940)

April 2017

List of molecular functions and their associated values for the present dataset. Table of all the va...

Additional file 8: of Biphasic modulation of insulin signaling enables highly efficient hematopoietic differentiation from human pluripotent stem cells

Fuyu Duan (3690385)
Rujin Huang (3690379)
Fengzhi Zhang (335439)
Yonglin Zhu (5567597)
Lin Wang (11986)
Xia Chen (299366)
Lufeng Bai (5567600)
Wei Guo (86150)
Sophia Chang (3690382)
Xiaoyu Hu (4159)
Jie Na (221422)

July 2018

Table S3. DEseq2 gene list of significantly differentially expressed genes in day 8 HSPCs and ECs (X...

Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Szucs, Matthew J
Ammendolia, Dustin A
MacMullan, Melanie A
Rakoff-Nahoum, Seth
Mead, Benjamin Elliott
Ordovas-Montanes, Jose Manuel
Braun, Alexandra Provost
Levy, Lauren
Saluja, Prerna Bhargava
Yin, Xiaolei
Hughes, Travis K.
Wadsworth, Marc Havens
Ahmad, Rushdy
Carr, Steven A
Langer, Robert S
Collins, James J.
Shalek, Alexander K
Karp, Jeffrey Michael

June 2018

Background Single-cell genomic methods now provide unprecedented resolution for cha...

Additional file 1: of Cell maps on the human genome

Christopher Cherniak (6492422)
Raul Rodriguez-Esteban (257885)

March 2019

Table S1. GeneCts per chromosome and cellular location. Gene entries include all subcellular targets...

Additional file 2: of Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis

Ji Dong (553653)
Yuqiong Hu (4963780)
Xiaoying Fan (3419693)
Xinglong Wu (1347408)
Yunuo Mao (4963774)
Boqiang Hu (3419696)
Hongshan Guo (4963777)
Lu Wen (385160)
Fuchou Tang (14392)

March 2018

Barcode-RT primer information, cell cycle gene list, and E-, M- and S-score gene list. (XLSX 18 kb

Additional file 3: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Benjamin Mead (5343608)
Jose Ordovas-Montanes (4805409)
Alexandra Braun (4862290)
Lauren Levy (5343611)
Prerna Bhargava (1572145)
Matthew Szucs (5343614)
Dustin Ammendolia (5343605)
Melanie MacMullan (5343617)
Xiaolei Yin (378829)
Travis Hughes (5343599)
Marc Wadsworth (5343602)
Rushdy Ahmad (443194)
Seth Rakoff-Nahoum (272894)
Steven Carr (5343596)
Robert Langer (166824)
James Collins (489526)
Alex Shalek (3424427)
Jeffrey Karp (1229817)

June 2018

Figure S1. Image analysis of cell clusters and flow cytometry. A Bright-field microscopy after 6 day...

Additional file 1: of Highly efficient and expedited hepatic differentiation from human pluripotent stem cells by pure small-molecule cocktails

Cong Du (2702083)
Yuan Feng (213823)
Dongbo Qiu (4927330)
Yan Xu (14594)
Mao Pang (710425)
Nan Cai (4927327)
Andy Xiang (3471293)
Qi Zhang (28502)

March 2018

Table S1. Small molecules used for hepatic differentiation. Table S2. Primers used to amplify the tr...

Additional file 1: of Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis

Ji Dong (553653)
Yuqiong Hu (4963780)
Xiaoying Fan (3419693)
Xinglong Wu (1347408)
Yunuo Mao (4963774)
Boqiang Hu (3419696)
Hongshan Guo (4963777)
Lu Wen (385160)
Fuchou Tang (14392)

March 2018

Figure S1. Quality control of the dataset and the characteristics of clusters. Figure S2. Interactio...

Additional file 1 of Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Xin Fang (134979)
Jonathan Monk (3548066)
Nathan Mih (3146436)
Bin Du (138774)
Anand Sastry (5369741)
Erol Kavvas (3465563)
Yara Seif (4908814)
Larry Smarr (379158)
Bernhard Palsson (450761)

June 2018

Table S1: Metadata of 110 strains. Table S2: Genes associated with mucus degradation. Table S3: Meta...

Additional file 3: of Enrichment of in vivo transcription data from dietary intervention studies with in vitro data provides improved insight into gene regulation mechanisms in the intestinal mucosa

Marcel Hulst (3122097)
Alfons Jansman (3849133)
Ilonka Wijers (3923252)
Arjan Hoekman (3122112)
StĂŠphanie Vastenhouw (3923261)
Marinus van Krimpen (3923249)
Mari Smits (3122115)
Dirkjan Schokker (579932)

April 2017

Table S3. Full names of overlapping DEGs expressed in vivo and in vitro ZnO, rye and amoxicillin int...

Additional file 7: of Comparative analysis of sequencing technologies for single-cell transcriptomics

Kedar Natarajan (3563123)
Zhichao Miao (838497)
Miaomiao Jiang (559714)
Xiaoyun Huang (659874)
Hongpo Zhou (6566438)
Jiarui Xie (6566441)
Chunqing Wang (3702286)
Shishang Qin (6566444)
Zhikun Zhao (6566447)
Liang Wu (131111)
Naibo Yang (3097908)
Bo Li (112195)
Yong Hou (420455)
Shiping Liu (79385)
Sarah Teichmann (3553601)

April 2019

Table S5. Single-cell library statistics computed from randomly downsampled 1 million paired-end seq...

Additional file 1: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Abstract

Extracted data

Additional file 1: of Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Abstract

Extracted data

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