MOESM1 of Xenograft tumors derived from malignant pleural effusion of the patients with non-small-cell lung cancer as models to explore drug resistance

Yunhua Xu (1794451)
Feifei Zhang (105135)
Xiaoqing Pan (202756)
Guan Wang (109695)
Lei Zhu (16642)
Jie Zhang (64655)
Danyi Wen (508019)
Shun Lu (402894)

Publication date

May 2018

DOI

10.6084/m9.figshare.6234419.v1

Abstract

Additional file 1: Table S1. Summary of whole exome sequencing data quality control for patient-derived biopsies and xenografts (paired-end read length 2âĂâ150 bp for all samples)

Extracted data

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Data Protection

MOESM1 of Xenograft tumors derived from malignant pleural effusion of the patients with non-small-cell lung cancer as models to explore drug resistance

Yunhua Xu (1794451)
Feifei Zhang (105135)
Xiaoqing Pan (202756)
Guan Wang (109695)
Lei Zhu (16642)
Jie Zhang (64655)
Danyi Wen (508019)
Shun Lu (402894)

Open link

Publication date

May 2018

DOI

10.6084/m9.figshare.6234419.v1

Abstract

Additional file 1: Table S1. Summary of whole exome sequencing data quality control for patient-derived biopsies and xenografts (paired-end read length 2âĂâ150 bp for all samples)

Extracted data

Kobe Reynders (5526461)
Els Wauters (101718)
Matthieu Moisse (659185)
Herbert DecaluwĂŠ (5526488)
Paul De Leyn (5526455)
StĂŠphanie Peeters (5526485)
Maarten Lambrecht (5526458)
Kristiaan Nackaerts (3210705)
Christophe Dooms (2938749)
Wim Janssens (101722)
Johan Vansteenkiste (5526467)
Diether Lambrechts (101772)
Dirk De Ruysscher (810406)

July 2018

Table S1. RNA-sequencing results for tumor tissue (a) or non-malignant lung tissue (b). Differential...

Additional file 2: Table S1, Table S2, Table S3, Table S4, Table S5, and Table S6. of Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

Silvia Bonfiglio (110384)
Irene Vanni (3487904)
Valeria Rossella (3487898)
Anna Truini (3487889)
Dejan Lazarevic (2541580)
Maria Giovanna Dal Bello (3487907)
Angela Alama (217640)
Marco Mora (3487895)
Erika Rijavec (3487892)
Carlo Genova (3487901)
Davide Cittaro (29939)
Francesco Grossi (371982)
Simona Coco (673158)

August 2016

Table S1. Sequencing metrics for libraries prepared with both Agilent SureSelect XT v.5 and Roche Ni...

Additional file 2: Table S2. of Whole exome sequencing of an asbestos-induced wild-type murine model of malignant mesothelioma

Sophie Sneddon (4064632)
Ann-Marie Patch (481815)
Ian Dick (3538622)
Stephen Kazakoff (4064629)
John Pearson (629146)
Nicola Waddell (481824)
Richard Allcock (382924)
Robert Holt (47255)
Bruce Robinson (147791)
Jenette Creaney (341814)

June 2017

Genes of interest previously reported in MM and primer sequences used to detect expression of the ta...

MOESM1 of Personalized treatment based on mini patient-derived xenografts and WES/RNA sequencing in a patient with metastatic duodenal adenocarcinoma

Peng Zhao (128233)
Hui Chen (28597)
Danyi Wen (508019)
Shuo Mou (5681804)
Feifei Zhang (105135)
Shusen Zheng (187083)

August 2018

Additional file 1: Table S1. Quality control metrics of targeted sequencing data. Table S2. Quality ...

MOESM1 of Patient-derived tumor immune microenvironments in patient-derived xenografts of lung cancer

Xingxiang Pu (663654)
Ran Zhang (117374)
Li Wang (15202)
Yungchang Chen (6010931)
Yi Xu (131145)
Apar Pataer (184395)
Ismail Meraz (6010934)
Xiaoshan Zhang (1411513)
Shuhong Wu (192478)
Lin Wu (153444)
Dan Su (8007)
Weimin Mao (550414)
John Heymach (5343626)
Jack Roth (3258858)
Stephen Swisher (5343632)
Bingliang Fang (184412)

November 2018

Additional file 1: Table S1. Clinical information of PDXs used for TIL studies. Table S2. Clinical i...

Additional file 3: Table S7 and Table S8. of Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

Silvia Bonfiglio (110384)
Irene Vanni (3487904)
Valeria Rossella (3487898)
Anna Truini (3487889)
Dejan Lazarevic (2541580)
Maria Giovanna Dal Bello (3487907)
Angela Alama (217640)
Marco Mora (3487895)
Erika Rijavec (3487892)
Carlo Genova (3487901)
Davide Cittaro (29939)
Francesco Grossi (371982)
Simona Coco (673158)

August 2016

Table S7. Mean coverage achieved by Agilent SureSelect and Roche NimbleGen libraries within 90 PCR-c...

Additional file 1: of Whole exome sequencing (WES) on formalin-fixed, paraffin-embedded (FFPE) tumor tissue in gastrointestinal stromal tumors (GIST)

Annalisa Astolfi (229848)
Milena Urbini (3517931)
Valentina Indio (3517925)
Margherita Nannini (3517922)
Chiara Genovese (3541631)
Donatella Santini (53947)
Maristella Saponara (3541634)
Anna Mandrioli (3541628)
Giorgio Ercolani (3541637)
Giovanni Brandi (314688)
Guido Biasco (314704)
Maria Pantaleo (3517928)

November 2015

Table S1. Clinical and biological data of the patients included in the study. Table S2. Tagmented DN...

Additional file 2: of XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

Roelof Kluin (5820728)
Kristel Kemper (362317)
Thomas Kuilman (682262)
Julian de Ruiter (5820731)
Vivek Iyer (572160)
Josep Forment (5820734)
Paulien Cornelissen-Steijger (167454)
Iris de Rink (5820737)
Petra ter Brugge (1677586)
Ji-Ying Song (167443)
Sjoerd Klarenbeek (5820740)
Ultan McDermott (213251)
Jos Jonkers (13239)
Arno Velds (23633)
David Adams (202540)
Daniel Peeper (5820743)
Oscar Krijgsman (680688)

October 2018

Table S2. Pathology estimate and SNVs of eight PDX samples. Percentage of mouse stromal cells, detec...

Additional file 1: of XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

Roelof Kluin (5820728)
Kristel Kemper (362317)
Thomas Kuilman (682262)
Julian de Ruiter (5820731)
Vivek Iyer (572160)
Josep Forment (5820734)
Paulien Cornelissen-Steijger (167454)
Iris de Rink (5820737)
Petra ter Brugge (1677586)
Ji-Ying Song (167443)
Sjoerd Klarenbeek (5820740)
Ultan McDermott (213251)
Jos Jonkers (13239)
Arno Velds (23633)
David Adams (202540)
Daniel Peeper (5820743)
Oscar Krijgsman (680688)

October 2018

Table S1. WGS of mouse strains mapped to human. Number of sequence reads from 3 mouse strains mapped...

Additional file 4: of XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

Roelof Kluin (5820728)
Kristel Kemper (362317)
Thomas Kuilman (682262)
Julian de Ruiter (5820731)
Vivek Iyer (572160)
Josep Forment (5820734)
Paulien Cornelissen-Steijger (167454)
Iris de Rink (5820737)
Petra ter Brugge (1677586)
Ji-Ying Song (167443)
Sjoerd Klarenbeek (5820740)
Ultan McDermott (213251)
Jos Jonkers (13239)
Arno Velds (23633)
David Adams (202540)
Daniel Peeper (5820743)
Oscar Krijgsman (680688)

October 2018

Figure S1. Performance of XenofilteR and Xenome on PDX samples. Mutation calling and read counts for...

MOESM1 of The genomics of desmoplastic small round cell tumor reveals the deregulation of genes related to DNA damage response, epithelial–mesenchymal transition, and immune response

Andrea Devecchi (3571553)
Loris De Cecco (107073)
Matteo Dugo (136516)
Donata Penso (3571544)
Gianpaolo Dagrada (5754221)
Silvia Brich (5754233)
Silvia Stacchiotti (6021296)
Marialuisa Sensi (6021299)
Silvana Canevari (136527)
Silvana Pilotti (355925)

November 2018

Additional file 1: Figure S1. Workflow of data processing and bioinformatics pipeline for whole-exom...

Additional file 4: Table S4. of Exosomes isolated from cancer patientsâ sera transfer malignant traits and confer the same phenotype of primary tumors to oncosuppressor-mutated cells

Mohamed Abdouh (181282)
Dana Hamam (3400181)
Zu-Hua Gao (329479)
Vincenzo Arena (3400187)
Manuel Arena (3400178)
Goffredo Arena (3400184)

August 2017

List of top 100 proteins that are often identified in exosomes (ExoCarta). (PDF 158 kb

Additional file 1: of Tag-based next generation sequencing: a feasible and reliable assay for EGFR T790M mutation detection in circulating tumor DNA of non small cell lung cancer patients

Mariella Dono (529161)
Giuseppa De Luca (6643022)
Sonia Lastraioli (6643025)
Giorgia Anselmi (6643028)
Maria Dal Bello (6643031)
Simona Coco (673158)
Irene Vanni (3487904)
Francesco Grossi (371982)
Antonella Vigani (6643034)
Carlo Genova (3487901)
Manlio Ferrarini (207820)
Jean Ravetti (6643037)
Simona Zupo (529162)

April 2019

Table S1. Clinical characteristics of the patientsâ cohort. Samples from 42 patients were availabl...

Additional file 1: of Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma

Xiaoyu Wang (182979)
Xiaohong Li (71964)
Yichen Cheng (3551063)
Xin Sun (127355)
Xibin Sun (644822)
Steve Self (123890)
Charles Kooperberg (18693)
James Dai (3551066)

September 2015

Supplementary tables. Table S1. Cancer genes in detected amplification regions. Table S2. Cancer gen...

Additional file 1: of Exome scale map of genetic alterations promoting metastasis in colorectal cancer

Krzysztof Goryca (240597)
Maria Kulecka (2503180)
Agnieszka Paziewska (170076)
Michalina Dabrowska (800221)
Marta Grzelak (5771918)
Magdalena Skrzypczak (240596)
Krzysztof Ginalski (8940)
Andrzej Mroz (5771921)
Andrzej Rutkowski (170103)
Katarzyna Paczkowska (5771924)
Michal Mikula (240599)
Jerzy Ostrowski (170111)

September 2018

Table S1. Sequencing parameters for 3 samples with the highest and 3 samples with the lowest sequenc...

Additional file 1: of RNA-sequencing in non-small cell lung cancer shows gene downregulation of therapeutic targets in tumor tissue compared to non-malignant lung tissue

Kobe Reynders (5526461)
Els Wauters (101718)
Matthieu Moisse (659185)
Herbert DecaluwĂŠ (5526488)
Paul De Leyn (5526455)
StĂŠphanie Peeters (5526485)
Maarten Lambrecht (5526458)
Kristiaan Nackaerts (3210705)
Christophe Dooms (2938749)
Wim Janssens (101722)
Johan Vansteenkiste (5526467)
Diether Lambrechts (101772)
Dirk De Ruysscher (810406)

July 2018

Table S1. RNA-sequencing results for tumor tissue (a) or non-malignant lung tissue (b). Differential...

Silvia Bonfiglio (110384)
Irene Vanni (3487904)
Valeria Rossella (3487898)
Anna Truini (3487889)
Dejan Lazarevic (2541580)
Maria Giovanna Dal Bello (3487907)
Angela Alama (217640)
Marco Mora (3487895)
Erika Rijavec (3487892)
Carlo Genova (3487901)
Davide Cittaro (29939)
Francesco Grossi (371982)
Simona Coco (673158)

August 2016

Table S1. Sequencing metrics for libraries prepared with both Agilent SureSelect XT v.5 and Roche Ni...

Additional file 2: Table S2. of Whole exome sequencing of an asbestos-induced wild-type murine model of malignant mesothelioma

Sophie Sneddon (4064632)
Ann-Marie Patch (481815)
Ian Dick (3538622)
Stephen Kazakoff (4064629)
John Pearson (629146)
Nicola Waddell (481824)
Richard Allcock (382924)
Robert Holt (47255)
Bruce Robinson (147791)
Jenette Creaney (341814)

June 2017

Genes of interest previously reported in MM and primer sequences used to detect expression of the ta...

MOESM1 of Patient-derived tumor immune microenvironments in patient-derived xenografts of lung cancer

Xingxiang Pu (663654)
Ran Zhang (117374)
Li Wang (15202)
Yungchang Chen (6010931)
Yi Xu (131145)
Apar Pataer (184395)
Ismail Meraz (6010934)
Xiaoshan Zhang (1411513)
Shuhong Wu (192478)
Lin Wu (153444)
Dan Su (8007)
Weimin Mao (550414)
John Heymach (5343626)
Jack Roth (3258858)
Stephen Swisher (5343632)
Bingliang Fang (184412)

November 2018

Additional file 1: Table S1. Clinical information of PDXs used for TIL studies. Table S2. Clinical i...

Additional file 3: Table S7 and Table S8. of Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples

Silvia Bonfiglio (110384)
Irene Vanni (3487904)
Valeria Rossella (3487898)
Anna Truini (3487889)
Dejan Lazarevic (2541580)
Maria Giovanna Dal Bello (3487907)
Angela Alama (217640)
Marco Mora (3487895)
Erika Rijavec (3487892)
Carlo Genova (3487901)
Davide Cittaro (29939)
Francesco Grossi (371982)
Simona Coco (673158)

August 2016

Table S7. Mean coverage achieved by Agilent SureSelect and Roche NimbleGen libraries within 90 PCR-c...

Additional file 1: of Whole exome sequencing (WES) on formalin-fixed, paraffin-embedded (FFPE) tumor tissue in gastrointestinal stromal tumors (GIST)

Annalisa Astolfi (229848)
Milena Urbini (3517931)
Valentina Indio (3517925)
Margherita Nannini (3517922)
Chiara Genovese (3541631)
Donatella Santini (53947)
Maristella Saponara (3541634)
Anna Mandrioli (3541628)
Giorgio Ercolani (3541637)
Giovanni Brandi (314688)
Guido Biasco (314704)
Maria Pantaleo (3517928)

November 2015

Table S1. Clinical and biological data of the patients included in the study. Table S2. Tagmented DN...

Additional file 2: of XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

Roelof Kluin (5820728)
Kristel Kemper (362317)
Thomas Kuilman (682262)
Julian de Ruiter (5820731)
Vivek Iyer (572160)
Josep Forment (5820734)
Paulien Cornelissen-Steijger (167454)
Iris de Rink (5820737)
Petra ter Brugge (1677586)
Ji-Ying Song (167443)
Sjoerd Klarenbeek (5820740)
Ultan McDermott (213251)
Jos Jonkers (13239)
Arno Velds (23633)
David Adams (202540)
Daniel Peeper (5820743)
Oscar Krijgsman (680688)

October 2018

Table S2. Pathology estimate and SNVs of eight PDX samples. Percentage of mouse stromal cells, detec...

Additional file 1: of XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

Roelof Kluin (5820728)
Kristel Kemper (362317)
Thomas Kuilman (682262)
Julian de Ruiter (5820731)
Vivek Iyer (572160)
Josep Forment (5820734)
Paulien Cornelissen-Steijger (167454)
Iris de Rink (5820737)
Petra ter Brugge (1677586)
Ji-Ying Song (167443)
Sjoerd Klarenbeek (5820740)
Ultan McDermott (213251)
Jos Jonkers (13239)
Arno Velds (23633)
David Adams (202540)
Daniel Peeper (5820743)
Oscar Krijgsman (680688)

October 2018

Table S1. WGS of mouse strains mapped to human. Number of sequence reads from 3 mouse strains mapped...

Additional file 4: of XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

Roelof Kluin (5820728)
Kristel Kemper (362317)
Thomas Kuilman (682262)
Julian de Ruiter (5820731)
Vivek Iyer (572160)
Josep Forment (5820734)
Paulien Cornelissen-Steijger (167454)
Iris de Rink (5820737)
Petra ter Brugge (1677586)
Ji-Ying Song (167443)
Sjoerd Klarenbeek (5820740)
Ultan McDermott (213251)
Jos Jonkers (13239)
Arno Velds (23633)
David Adams (202540)
Daniel Peeper (5820743)
Oscar Krijgsman (680688)

October 2018

Figure S1. Performance of XenofilteR and Xenome on PDX samples. Mutation calling and read counts for...

MOESM1 of The genomics of desmoplastic small round cell tumor reveals the deregulation of genes related to DNA damage response, epithelial–mesenchymal transition, and immune response

Andrea Devecchi (3571553)
Loris De Cecco (107073)
Matteo Dugo (136516)
Donata Penso (3571544)
Gianpaolo Dagrada (5754221)
Silvia Brich (5754233)
Silvia Stacchiotti (6021296)
Marialuisa Sensi (6021299)
Silvana Canevari (136527)
Silvana Pilotti (355925)

November 2018

Additional file 1: Figure S1. Workflow of data processing and bioinformatics pipeline for whole-exom...

Additional file 4: Table S4. of Exosomes isolated from cancer patientsâ sera transfer malignant traits and confer the same phenotype of primary tumors to oncosuppressor-mutated cells

Mohamed Abdouh (181282)
Dana Hamam (3400181)
Zu-Hua Gao (329479)
Vincenzo Arena (3400187)
Manuel Arena (3400178)
Goffredo Arena (3400184)

August 2017

List of top 100 proteins that are often identified in exosomes (ExoCarta). (PDF 158 kb

Additional file 1: of Tag-based next generation sequencing: a feasible and reliable assay for EGFR T790M mutation detection in circulating tumor DNA of non small cell lung cancer patients

Mariella Dono (529161)
Giuseppa De Luca (6643022)
Sonia Lastraioli (6643025)
Giorgia Anselmi (6643028)
Maria Dal Bello (6643031)
Simona Coco (673158)
Irene Vanni (3487904)
Francesco Grossi (371982)
Antonella Vigani (6643034)
Carlo Genova (3487901)
Manlio Ferrarini (207820)
Jean Ravetti (6643037)
Simona Zupo (529162)

April 2019

Table S1. Clinical characteristics of the patientsâ cohort. Samples from 42 patients were availabl...

Additional file 1: of Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma

Xiaoyu Wang (182979)
Xiaohong Li (71964)
Yichen Cheng (3551063)
Xin Sun (127355)
Xibin Sun (644822)
Steve Self (123890)
Charles Kooperberg (18693)
James Dai (3551066)

September 2015

Supplementary tables. Table S1. Cancer genes in detected amplification regions. Table S2. Cancer gen...

Additional file 1: of Exome scale map of genetic alterations promoting metastasis in colorectal cancer

Krzysztof Goryca (240597)
Maria Kulecka (2503180)
Agnieszka Paziewska (170076)
Michalina Dabrowska (800221)
Marta Grzelak (5771918)
Magdalena Skrzypczak (240596)
Krzysztof Ginalski (8940)
Andrzej Mroz (5771921)
Andrzej Rutkowski (170103)
Katarzyna Paczkowska (5771924)
Michal Mikula (240599)
Jerzy Ostrowski (170111)

September 2018

Table S1. Sequencing parameters for 3 samples with the highest and 3 samples with the lowest sequenc...

Additional file 1: of RNA-sequencing in non-small cell lung cancer shows gene downregulation of therapeutic targets in tumor tissue compared to non-malignant lung tissue

Kobe Reynders (5526461)
Els Wauters (101718)
Matthieu Moisse (659185)
Herbert DecaluwĂŠ (5526488)
Paul De Leyn (5526455)
StĂŠphanie Peeters (5526485)
Maarten Lambrecht (5526458)
Kristiaan Nackaerts (3210705)
Christophe Dooms (2938749)
Wim Janssens (101722)
Johan Vansteenkiste (5526467)
Diether Lambrechts (101772)
Dirk De Ruysscher (810406)

July 2018

Table S1. RNA-sequencing results for tumor tissue (a) or non-malignant lung tissue (b). Differential...

Silvia Bonfiglio (110384)
Irene Vanni (3487904)
Valeria Rossella (3487898)
Anna Truini (3487889)
Dejan Lazarevic (2541580)
Maria Giovanna Dal Bello (3487907)
Angela Alama (217640)
Marco Mora (3487895)
Erika Rijavec (3487892)
Carlo Genova (3487901)
Davide Cittaro (29939)
Francesco Grossi (371982)
Simona Coco (673158)

August 2016

Table S1. Sequencing metrics for libraries prepared with both Agilent SureSelect XT v.5 and Roche Ni...

Additional file 2: Table S2. of Whole exome sequencing of an asbestos-induced wild-type murine model of malignant mesothelioma

Sophie Sneddon (4064632)
Ann-Marie Patch (481815)
Ian Dick (3538622)
Stephen Kazakoff (4064629)
John Pearson (629146)
Nicola Waddell (481824)
Richard Allcock (382924)
Robert Holt (47255)
Bruce Robinson (147791)
Jenette Creaney (341814)

June 2017

Genes of interest previously reported in MM and primer sequences used to detect expression of the ta...

MOESM1 of Xenograft tumors derived from malignant pleural effusion of the patients with non-small-cell lung cancer as models to explore drug resistance

Abstract

Extracted data

MOESM1 of Xenograft tumors derived from malignant pleural effusion of the patients with non-small-cell lung cancer as models to explore drug resistance

Abstract

Extracted data

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