Additional file 2: of RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

Additional file 7 of Combining single-cell RNA sequencing of peripheral blood mononuclear cells and exosomal transcriptome to reveal the cellular and genetic profiles in COPD

Yanli Pei (5505332)
Yuxi Wei (635013)
Boshizhang Peng (13838453)
Mengqi Wang (421473)
Wei Xu (28953)
Zhe Chen (196097)
Xindi Ke (11333195)
Lei Rong (1488667)

September 2022

Additional file 7: Fig. S3. Functional analysis of DEGs in other clusters between patients with COPD...

Additional file 2: of Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis

Rosa Faner (564671)
Jarrett Morrow (662723)
Sandra Casas-Recasens (6187661)
Suzanne Cloonan (6187664)
Guillaume Noell (4503412)
Alejandra LĂłpez-Giraldo (6187667)
Ruth Tal-Singer (164946)
Bruce Miller (695078)
Edwin Silverman (758792)
Alvar AgustĂ (5396321)
Craig Hersh (3457529)

January 2019

Figure S1. Association between blood gene modules and lung function. The module definition was perfo...

Additional file 1: of Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility

Shannon Bruse (3481571)
Michael Moreau (3481577)
Yana Bromberg (51423)
Jun-Ho Jang (748271)
Nan Wang (21935)
Hongseok Ha (3400535)
Maria Picchi (3481559)
Yong Lin (177139)
Raymond Langley (3481580)
Clifford Qualls (117765)
Julia Klensney-Tait (3481565)
Joseph Zabner (138271)
Shuguang Leng (173462)
Jenny Mao (3481568)
Steven Belinsky (3481562)
Jinchuan Xing (11012)
Toru Nyunoya (3481574)

January 2016

COPD candidate genes prioritized by the VAAST analysis. Results from different VAAST run settings (T...

Additional file 1: of RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

Jarrett Morrow (662723)
Robert Chase (1436653)
Margaret Parker (3457517)
Kimberly Glass (416881)
Minseok Seo (316795)
Miguel Divo (2621386)
Caroline Owen (6548522)
Peter Castaldi (2993694)
Dawn DeMeo (3115695)
Edwin Silverman (758792)
Craig Hersh (3457529)

April 2019

Supplemental Figures: Additional figures to support the findings of this study. (PDF 780 kb

Additional file 3: of RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

Jarrett Morrow (662723)
Robert Chase (1436653)
Margaret Parker (3457517)
Kimberly Glass (416881)
Minseok Seo (316795)
Miguel Divo (2621386)
Caroline Owen (6548522)
Peter Castaldi (2993694)
Dawn DeMeo (3115695)
Edwin Silverman (758792)
Craig Hersh (3457529)

April 2019

Supplemental Tables: Additional tables to support the findings of this study. Table S4. Differential...

Additional file 2 of Combining single-cell RNA sequencing of peripheral blood mononuclear cells and exosomal transcriptome to reveal the cellular and genetic profiles in COPD

Yanli Pei (5505332)
Yuxi Wei (635013)
Boshizhang Peng (13838453)
Mengqi Wang (421473)
Wei Xu (28953)
Zhe Chen (196097)
Xindi Ke (11333195)
Lei Rong (1488667)

September 2022

Additional file 2: Table S2. Exosomal differentially expressed mRNA between COPD patient and healthy...

RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

Jarrett D. Morrow
Robert P. Chase
Margaret M. Parker
Kimberly Glass
Minseok Seo
Miguel Divo
Caroline A. Owen
Peter Castaldi
Dawn L. DeMeo
Edwin K. Silverman
Craig P. Hersh

April 2019

Abstract Background Multiple gene expression studies have been performed separately in peripheral bl...

Additional file 4 of Combining single-cell RNA sequencing of peripheral blood mononuclear cells and exosomal transcriptome to reveal the cellular and genetic profiles in COPD

Yanli Pei (5505332)
Yuxi Wei (635013)
Boshizhang Peng (13838453)
Mengqi Wang (421473)
Wei Xu (28953)
Zhe Chen (196097)
Xindi Ke (11333195)
Lei Rong (1488667)

September 2022

Additional file 4: Table S5. Pairs of mRNA-miRNA predicted by TargetScan. Table S6. Pairs of lncRNA-...

Additional file 1 of Ex-vivo RNA expression analysis of vaccine candidate genes in COPD sputum samples

Cecilia Brettoni (401097)
Alessandro Muzzi (216475)
Simona Rondini (82372)
Vincent Weynants (13010397)
Silvia Rossi Paccani (374038)

October 2023

Additional file 1: Table S1. PCR primer sequences for NTHi and Mcat genes. Figure S1. NTHi gene RNA ...

Additional file 1: of RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs

Jiyoun Yeo (448396)
Diego Morales (760820)
Tian Chen (550371)
Erin Crawford (3995537)
Xiaolu Zhang (433873)
Thomas Blomquist (3995534)
Albert Levin (483979)
Pierre Massion (4913062)
Douglas Arenberg (4913056)
David Midthun (4622974)
Peter Mazzone (4031270)
Steven Nathan (4913053)
Ronald Wainz (4913068)
Patrick Nana-Sinkam (425104)
Paige Willey (4913065)
Taylor Arend (4913074)
Karanbir Padda (4913077)
Shuhao Qiu (4070320)
Alexei Federov (4913071)
Dawn-Alita Hernandez (71925)
Jeffrey Hammersley (4913080)
Youngsook Yoon (71926)
Fadi Safi (4913059)
Sadik Khuder (86473)
James Willey (3995531)

March 2018

Tables S1, S2, S3, S4, S5 and S6. Table S1. This table provides: a) Gene-specific assay information ...

Additional file 1: of Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease

Hans Matsson (217735)
Cilla Söderhäll (117617)
Elisabet Einarsdottir (359261)
Maxime Lamontagne (116448)
Sanna Gudmundsson (3499502)
Helena Backman (3499499)
Anne Lindberg (3442631)
Eva Rönmark (764539)
Juha Kere (11900)
Don Sin (128552)
Dirkje Postma (3410420)
Yohan Bossé (69571)
Bo Lundbäck (154245)
Joakim Klar (549023)

November 2016

Supplementary methods. Detailed methods description regarding classification of COPD, sequencing pro...

Additional file 4: of Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility

Shannon Bruse (3481571)
Michael Moreau (3481577)
Yana Bromberg (51423)
Jun-Ho Jang (748271)
Nan Wang (21935)
Hongseok Ha (3400535)
Maria Picchi (3481559)
Yong Lin (177139)
Raymond Langley (3481580)
Clifford Qualls (117765)
Julia Klensney-Tait (3481565)
Joseph Zabner (138271)
Shuguang Leng (173462)
Jenny Mao (3481568)
Steven Belinsky (3481562)
Jinchuan Xing (11012)
Toru Nyunoya (3481574)

January 2016

siRNA screening in vitro analysis for 81 COPD candidate genes. For the 81 candidate genes, the detai...

Additional file 3: of Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility

Shannon Bruse (3481571)
Michael Moreau (3481577)
Yana Bromberg (51423)
Jun-Ho Jang (748271)
Nan Wang (21935)
Hongseok Ha (3400535)
Maria Picchi (3481559)
Yong Lin (177139)
Raymond Langley (3481580)
Clifford Qualls (117765)
Julia Klensney-Tait (3481565)
Joseph Zabner (138271)
Shuguang Leng (173462)
Jenny Mao (3481568)
Steven Belinsky (3481562)
Jinchuan Xing (11012)
Toru Nyunoya (3481574)

January 2016

The abundance of gene expression in primary human epithelial cell cultures using RNA-Seq. Expression...

Additional file 6 of Combining single-cell RNA sequencing of peripheral blood mononuclear cells and exosomal transcriptome to reveal the cellular and genetic profiles in COPD

Yanli Pei (5505332)
Yuxi Wei (635013)
Boshizhang Peng (13838453)
Mengqi Wang (421473)
Wei Xu (28953)
Zhe Chen (196097)
Xindi Ke (11333195)
Lei Rong (1488667)

September 2022

Additional file 6: Table S8. Single-cell differentially expressed mRNA in overall cells between COPD...

Additional file 5 of Combining single-cell RNA sequencing of peripheral blood mononuclear cells and exosomal transcriptome to reveal the cellular and genetic profiles in COPD

Yanli Pei (5505332)
Yuxi Wei (635013)
Boshizhang Peng (13838453)
Mengqi Wang (421473)
Wei Xu (28953)
Zhe Chen (196097)
Xindi Ke (11333195)
Lei Rong (1488667)

September 2022

Additional file 5: Fig. S2. Functional analysis of marker genes in other clusters. Bubble plot of KE...

Additional file 7 of Combining single-cell RNA sequencing of peripheral blood mononuclear cells and exosomal transcriptome to reveal the cellular and genetic profiles in COPD

Yanli Pei (5505332)
Yuxi Wei (635013)
Boshizhang Peng (13838453)
Mengqi Wang (421473)
Wei Xu (28953)
Zhe Chen (196097)
Xindi Ke (11333195)
Lei Rong (1488667)

September 2022

Additional file 7: Fig. S3. Functional analysis of DEGs in other clusters between patients with COPD...

Additional file 2: of Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis

Rosa Faner (564671)
Jarrett Morrow (662723)
Sandra Casas-Recasens (6187661)
Suzanne Cloonan (6187664)
Guillaume Noell (4503412)
Alejandra LĂłpez-Giraldo (6187667)
Ruth Tal-Singer (164946)
Bruce Miller (695078)
Edwin Silverman (758792)
Alvar AgustĂ (5396321)
Craig Hersh (3457529)

January 2019

Figure S1. Association between blood gene modules and lung function. The module definition was perfo...

Additional file 1: of Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility

Shannon Bruse (3481571)
Michael Moreau (3481577)
Yana Bromberg (51423)
Jun-Ho Jang (748271)
Nan Wang (21935)
Hongseok Ha (3400535)
Maria Picchi (3481559)
Yong Lin (177139)
Raymond Langley (3481580)
Clifford Qualls (117765)
Julia Klensney-Tait (3481565)
Joseph Zabner (138271)
Shuguang Leng (173462)
Jenny Mao (3481568)
Steven Belinsky (3481562)
Jinchuan Xing (11012)
Toru Nyunoya (3481574)

January 2016

COPD candidate genes prioritized by the VAAST analysis. Results from different VAAST run settings (T...

Additional file 1: of RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

Jarrett Morrow (662723)
Robert Chase (1436653)
Margaret Parker (3457517)
Kimberly Glass (416881)
Minseok Seo (316795)
Miguel Divo (2621386)
Caroline Owen (6548522)
Peter Castaldi (2993694)
Dawn DeMeo (3115695)
Edwin Silverman (758792)
Craig Hersh (3457529)

April 2019

Supplemental Figures: Additional figures to support the findings of this study. (PDF 780 kb

Additional file 3: of RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

Jarrett Morrow (662723)
Robert Chase (1436653)
Margaret Parker (3457517)
Kimberly Glass (416881)
Minseok Seo (316795)
Miguel Divo (2621386)
Caroline Owen (6548522)
Peter Castaldi (2993694)
Dawn DeMeo (3115695)
Edwin Silverman (758792)
Craig Hersh (3457529)

April 2019

Supplemental Tables: Additional tables to support the findings of this study. Table S4. Differential...

Additional file 2 of Combining single-cell RNA sequencing of peripheral blood mononuclear cells and exosomal transcriptome to reveal the cellular and genetic profiles in COPD

Yanli Pei (5505332)
Yuxi Wei (635013)
Boshizhang Peng (13838453)
Mengqi Wang (421473)
Wei Xu (28953)
Zhe Chen (196097)
Xindi Ke (11333195)
Lei Rong (1488667)

September 2022

Additional file 2: Table S2. Exosomal differentially expressed mRNA between COPD patient and healthy...

RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

Jarrett D. Morrow
Robert P. Chase
Margaret M. Parker
Kimberly Glass
Minseok Seo
Miguel Divo
Caroline A. Owen
Peter Castaldi
Dawn L. DeMeo
Edwin K. Silverman
Craig P. Hersh

April 2019

Abstract Background Multiple gene expression studies have been performed separately in peripheral bl...

Additional file 4 of Combining single-cell RNA sequencing of peripheral blood mononuclear cells and exosomal transcriptome to reveal the cellular and genetic profiles in COPD

Yanli Pei (5505332)
Yuxi Wei (635013)
Boshizhang Peng (13838453)
Mengqi Wang (421473)
Wei Xu (28953)
Zhe Chen (196097)
Xindi Ke (11333195)
Lei Rong (1488667)

September 2022

Additional file 4: Table S5. Pairs of mRNA-miRNA predicted by TargetScan. Table S6. Pairs of lncRNA-...

Additional file 1 of Ex-vivo RNA expression analysis of vaccine candidate genes in COPD sputum samples

Cecilia Brettoni (401097)
Alessandro Muzzi (216475)
Simona Rondini (82372)
Vincent Weynants (13010397)
Silvia Rossi Paccani (374038)

October 2023

Additional file 1: Table S1. PCR primer sequences for NTHi and Mcat genes. Figure S1. NTHi gene RNA ...

Additional file 1: of RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs

Jiyoun Yeo (448396)
Diego Morales (760820)
Tian Chen (550371)
Erin Crawford (3995537)
Xiaolu Zhang (433873)
Thomas Blomquist (3995534)
Albert Levin (483979)
Pierre Massion (4913062)
Douglas Arenberg (4913056)
David Midthun (4622974)
Peter Mazzone (4031270)
Steven Nathan (4913053)
Ronald Wainz (4913068)
Patrick Nana-Sinkam (425104)
Paige Willey (4913065)
Taylor Arend (4913074)
Karanbir Padda (4913077)
Shuhao Qiu (4070320)
Alexei Federov (4913071)
Dawn-Alita Hernandez (71925)
Jeffrey Hammersley (4913080)
Youngsook Yoon (71926)
Fadi Safi (4913059)
Sadik Khuder (86473)
James Willey (3995531)

March 2018

Tables S1, S2, S3, S4, S5 and S6. Table S1. This table provides: a) Gene-specific assay information ...

Additional file 1: of Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease

Hans Matsson (217735)
Cilla Söderhäll (117617)
Elisabet Einarsdottir (359261)
Maxime Lamontagne (116448)
Sanna Gudmundsson (3499502)
Helena Backman (3499499)
Anne Lindberg (3442631)
Eva Rönmark (764539)
Juha Kere (11900)
Don Sin (128552)
Dirkje Postma (3410420)
Yohan Bossé (69571)
Bo Lundbäck (154245)
Joakim Klar (549023)

November 2016

Supplementary methods. Detailed methods description regarding classification of COPD, sequencing pro...

Additional file 4: of Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility

Shannon Bruse (3481571)
Michael Moreau (3481577)
Yana Bromberg (51423)
Jun-Ho Jang (748271)
Nan Wang (21935)
Hongseok Ha (3400535)
Maria Picchi (3481559)
Yong Lin (177139)
Raymond Langley (3481580)
Clifford Qualls (117765)
Julia Klensney-Tait (3481565)
Joseph Zabner (138271)
Shuguang Leng (173462)
Jenny Mao (3481568)
Steven Belinsky (3481562)
Jinchuan Xing (11012)
Toru Nyunoya (3481574)

January 2016

siRNA screening in vitro analysis for 81 COPD candidate genes. For the 81 candidate genes, the detai...

Additional file 3: of Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility

Shannon Bruse (3481571)
Michael Moreau (3481577)
Yana Bromberg (51423)
Jun-Ho Jang (748271)
Nan Wang (21935)
Hongseok Ha (3400535)
Maria Picchi (3481559)
Yong Lin (177139)
Raymond Langley (3481580)
Clifford Qualls (117765)
Julia Klensney-Tait (3481565)
Joseph Zabner (138271)
Shuguang Leng (173462)
Jenny Mao (3481568)
Steven Belinsky (3481562)
Jinchuan Xing (11012)
Toru Nyunoya (3481574)

January 2016

The abundance of gene expression in primary human epithelial cell cultures using RNA-Seq. Expression...

Additional file 6 of Combining single-cell RNA sequencing of peripheral blood mononuclear cells and exosomal transcriptome to reveal the cellular and genetic profiles in COPD

Yanli Pei (5505332)
Yuxi Wei (635013)
Boshizhang Peng (13838453)
Mengqi Wang (421473)
Wei Xu (28953)
Zhe Chen (196097)
Xindi Ke (11333195)
Lei Rong (1488667)

September 2022

Additional file 6: Table S8. Single-cell differentially expressed mRNA in overall cells between COPD...

Additional file 5 of Combining single-cell RNA sequencing of peripheral blood mononuclear cells and exosomal transcriptome to reveal the cellular and genetic profiles in COPD

Yanli Pei (5505332)
Yuxi Wei (635013)
Boshizhang Peng (13838453)
Mengqi Wang (421473)
Wei Xu (28953)
Zhe Chen (196097)
Xindi Ke (11333195)
Lei Rong (1488667)

September 2022

Additional file 5: Fig. S2. Functional analysis of marker genes in other clusters. Bubble plot of KE...

Additional file 7 of Combining single-cell RNA sequencing of peripheral blood mononuclear cells and exosomal transcriptome to reveal the cellular and genetic profiles in COPD

Yanli Pei (5505332)
Yuxi Wei (635013)
Boshizhang Peng (13838453)
Mengqi Wang (421473)
Wei Xu (28953)
Zhe Chen (196097)
Xindi Ke (11333195)
Lei Rong (1488667)

September 2022

Additional file 7: Fig. S3. Functional analysis of DEGs in other clusters between patients with COPD...

Additional file 2: of Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis

Rosa Faner (564671)
Jarrett Morrow (662723)
Sandra Casas-Recasens (6187661)
Suzanne Cloonan (6187664)
Guillaume Noell (4503412)
Alejandra LĂłpez-Giraldo (6187667)
Ruth Tal-Singer (164946)
Bruce Miller (695078)
Edwin Silverman (758792)
Alvar AgustĂ (5396321)
Craig Hersh (3457529)

January 2019

Figure S1. Association between blood gene modules and lung function. The module definition was perfo...

Additional file 1: of Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility

Shannon Bruse (3481571)
Michael Moreau (3481577)
Yana Bromberg (51423)
Jun-Ho Jang (748271)
Nan Wang (21935)
Hongseok Ha (3400535)
Maria Picchi (3481559)
Yong Lin (177139)
Raymond Langley (3481580)
Clifford Qualls (117765)
Julia Klensney-Tait (3481565)
Joseph Zabner (138271)
Shuguang Leng (173462)
Jenny Mao (3481568)
Steven Belinsky (3481562)
Jinchuan Xing (11012)
Toru Nyunoya (3481574)

January 2016

COPD candidate genes prioritized by the VAAST analysis. Results from different VAAST run settings (T...

Additional file 2: of RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

Abstract

Extracted data

Additional file 2: of RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD

Abstract

Extracted data

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