Additional file 5: of Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Additional file 3: of Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD

Rachel Clifford (4913317)
Nick Fishbane (517664)
Jamie Patel (4913314)
Julia MacIsaac (3575030)
Lisa McEwen (3968174)
Andrew Fisher (1673086)
Corry-Anke Brandsma (41865)
Parameswaran Nair (463763)
Michael Kobor (3470795)
Tillie-Louise Hackett (92016)
Alan Knox (456628)

March 2018

Figure S1. (.EPS): CpG methylation variation in parenchymal fibroblasts in COPD samples. A) Plot of ...

DNA Methylome Alterations are Associated with Airway Macrophage Differentiation and Phenotype During Lung Fibrosis.

McErlean, P
Bell, CG
Hewitt, RJ
Busharat, Z
Ogger, PP
Ghai, P
Albers, GJ
Calamita, E
Kingston, S
Molyneaux, PL
Beck, S
Lloyd, CM
Maher, TM
Byrne, AJ

July 2021

RATIONALE: Airway macrophages (AMs) are key regulators of the lung environment and are implicated in...

Additional file 5: of Genome-wide analysis of DNA methylation in bronchial washings

Sang-Won Um (535627)
Yujin Kim (483088)
Bo Lee (3463586)
Dongho Kim (29790)
Kyung-Jong Lee (5237399)
Hong Kim (101826)
Joungho Han (483091)
Hojoong Kim (535625)
Young Shim (3463580)
Duk-Hwan Kim (483093)

May 2018

Table S3. The correlation between pack-years of smoking and DNA methylation in 53 control groups. (D...

Additional file 1: of Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Youdinghuan Chen (6067190)
David Armstrong (109098)
Lucas Salas (3711079)
Haley Hazlett (4055179)
Amanda Nymon (3203016)
John Dessaint (6067199)
Daniel Aridgides (380663)
Diane Mellinger (6067205)
Xiaoying Liu (192486)
Brock Christensen (3472082)
Alix Ashare (2549707)

December 2018

Table S1. Top hypo- and hyper-methylated CpGs in CF that are associated with known genes. (DOCX 17Â ...

Additional file 3: of Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Youdinghuan Chen (6067190)
David Armstrong (109098)
Lucas Salas (3711079)
Haley Hazlett (4055179)
Amanda Nymon (3203016)
John Dessaint (6067199)
Daniel Aridgides (380663)
Diane Mellinger (6067205)
Xiaoying Liu (192486)
Brock Christensen (3472082)
Alix Ashare (2549707)

December 2018

Table S2. Targeted next-generation bisulfite sequencing of EPIC identified genes. (DOCX 15Â kb

Additional file 2: of Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Youdinghuan Chen (6067190)
David Armstrong (109098)
Lucas Salas (3711079)
Haley Hazlett (4055179)
Amanda Nymon (3203016)
John Dessaint (6067199)
Daniel Aridgides (380663)
Diane Mellinger (6067205)
Xiaoying Liu (192486)
Brock Christensen (3472082)
Alix Ashare (2549707)

December 2018

Figure S1. Human leukocyte-specific protein-1 (LSP1) gene targeted next-generation sequencing (tNGS)...

Additional file 2: Figure S2. of DNA methylation at modifier genes of lung disease severity is altered in cystic fibrosis

Milena Magalhães (3747409)
Isabelle Rivals (144406)
Mireille Claustres (10836)
Jessica Varilh (396831)
Mélodie Thomasset (3747403)
Anne Bergougnoux (3747412)
Laurent Mely (3747415)
Sylvie Leroy (175152)
Harriet Corvol (313303)
Loïc Guillot (41929)
Marlène Murris (3747406)
Emmanuelle Beyne (72051)
Davide Caimmi (3747400)
Isabelle Vachier (3526700)
Raphaël Chiron (321612)
Albertina De Sario (222714)

February 2017

DNA methylation distribution at 14 analyzed genes in CF and control samples. (PDF 212 kb

Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Youdinghuan Chen
David A. Armstrong
Lucas A. Salas
Haley F. Hazlett
Amanda B. Nymon
John A. Dessaint
Daniel S. Aridgides
Diane L. Mellinger
Xiaoying Liu
Brock C. Christensen
Alix Ashare

December 2018

Abstract Background Lung macrophages are major participants in the pulmonary innate immune response....

Additional file 3: Figure S2. of Genome-wide DNA methylation profiling reveals novel epigenetic signatures in squamous cell lung cancer

Yuan-Xiang Shi (4614283)
Ying Wang (11406)
Xi Li (19208)
Wei Zhang (405)
Hong-Hao Zhou (156418)
Ji-Ye Yin (156407)
Zhao-Qian Liu (156422)

November 2017

Genomic context of CpG methylation. (A) The overall distribution of methylation sites in tumor versu...

Additional file 1: of Genome-wide DNA methylation profiling in whole blood reveals epigenetic signatures associated with migraine

Zachary Gerring (4787301)
Allan McRae (3400103)
Grant Montgomery (16569)
Dale Nyholt (4787298)

January 2018

Differentially methylated regions identified by a sliding window analysis. This file contains the ge...

Additional file 9: Table S8. of DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases

Symen Ligthart (701678)
Carola Marzi (236979)
Stella Aslibekyan (123439)
Michael Mendelson (2697424)
Karen Conneely (3448694)
Toshiko Tanaka (174638)
Elena Colicino (3503048)
Lindsay Waite (3503021)
Roby Joehanes (560601)
Weihua Guan (345071)
Jennifer Brody (174723)
Cathy Elks (3503054)
Riccardo Marioni (669892)
Min Jhun (3503015)
Golareh Agha (3503030)
Jan Bressler (248795)
Cavin Ward-Caviness (3503057)
Brian Chen (149932)
Tianxiao Huan (599733)
Kelly Bakulski (3503063)
Elias Salfati (3503045)
Giovanni Fiorito (136942)
Simone Wahl (112749)
Katharina Schramm (528479)
Jin Sha (847984)
Dena Hernandez (215322)
Allan Just (3448679)
Jennifer Smith (172056)
Nona Sotoodehnia (143373)
Luke Pilling (3503024)
James Pankow (160621)
Phil Tsao (3503066)
Chunyu Liu (9855)
Wei Zhao (14321)
Simonetta Guarrera (136940)
Vasiliki Michopoulos (3503051)
Alicia Smith (3448658)
Marjolein Peters (3503033)
David Melzer (202058)
Pantel Vokonas (587472)
Myriam Fornage (45591)
Holger Prokisch (26590)
Joshua Bis (711982)
Audrey Chu (3503069)
Christian Herder (44905)
Harald Grallert (72666)
Chen Yao (137375)
Sonia Shah (142603)
Allan McRae (3400103)
Honghuang Lin (560598)
Steve Horvath (28847)
Daniele Fallin (3503039)
Albert Hofman (107303)
Nicholas Wareham (153226)
Kerri Wiggins (3503018)
Andrew Feinberg (242567)
John Starr (231855)
Peter Visscher (3400094)
Joanne Murabito (3503036)
Sharon Kardia (3503060)
Devin Absher (217357)
Elisabeth Binder (3448661)
Andrew Singleton (23294)
Stefania Bandinelli (150002)
Annette Peters (62601)
Melanie Waldenberger (236985)
Giuseppe Matullo (136983)
Joel Schwartz (18324)
Ellen Demerath (198657)
AndrĂŠ Uitterlinden (3404267)
Joyce van Meurs (3404240)
Oscar Franco (2885594)
Yii-Der Chen (3503075)
Daniel Levy (51573)
Stephen Turner (3503027)
Ian Deary (489588)
Kerry Ressler (3503072)
JosĂŠe Dupuis (3503084)
Luigi Ferrucci (150038)
Ken Ong (448067)
Themistocles Assimes (746456)
Eric Boerwinkle (36288)
Wolfgang Koenig (26222)
Donna Arnett (192289)
Andrea Baccarelli (36523)
Emelia Benjamin (3503042)
Abbas Dehghan (174878)

December 2016

Significant methylation-expression results and corresponding expression-CRP results for the replicat...

Additional file 1: of Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD

Rachel Clifford (4913317)
Nick Fishbane (517664)
Jamie Patel (4913314)
Julia MacIsaac (3575030)
Lisa McEwen (3968174)
Andrew Fisher (1673086)
Corry-Anke Brandsma (41865)
Parameswaran Nair (463763)
Michael Kobor (3470795)
Tillie-Louise Hackett (92016)
Alan Knox (456628)

March 2018

Table S1. (.MWD): DNA regions differentially methylated with COPD status in airway fibroblasts. Summ...

Additional file 2 of An epigenetic and transcriptomic signature of immune tolerance in human monocytes through multi-omics integration

Xanthe Brands (8802716)
Bastiaan W. Haak (8802719)
Augustijn M. Klarenbeek (8802722)
Joe Butler (4331395)
Fabrice Uhel (3682579)
Wanhai Qin (10515966)
Natasja A. Otto (8802725)
Marja E. Jakobs (11282828)
Daniël R. Faber (8802728)
René Lutter (3407615)
W. Joost Wiersinga (8802734)
Tom van der Poll (33907)
Brendon P. Scicluna (8802731)

August 2021

Additional file 2: Supplementary figures (Fig. S1 – S5). Fig. S1: Flow cytometry analysis of purifie...

Additional file 5: Table S4. of DNA methylation profiling in peripheral lung tissues of smokers and patients with COPD

Isaac Sundar (3927785)
Qiangzong Yin (3927788)
Brian Baier (517434)
Li Yan (107001)
Witold Mazur (2118115)
Dongmei Li (176178)
Martha Susiarjo (23984)
Irfan Rahman (333928)

April 2017

CpGs differentially methylated in lung DNA in relation to smokers vs. non-smokers (Pâ<â0.01). (C...

DNA methylome alterations are associated with airway macrophage differentiation and phenotype during lung fibrosis.

McErlean, P
Bell, CG
Hewitt, RJ
Busharat, Z
Ogger, PP
Ghai, P
Albers, GJ
Calamita, E
Kingston, S
Molyneaux, PL
Beck, S
Lloyd, CM
Maher, TM
Byrne, AJ

July 2021

Rationale: Airway macrophages (AMs) are key regulators of the lung environment and are implicated in...

Additional file 3: of Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD

Rachel Clifford (4913317)
Nick Fishbane (517664)
Jamie Patel (4913314)
Julia MacIsaac (3575030)
Lisa McEwen (3968174)
Andrew Fisher (1673086)
Corry-Anke Brandsma (41865)
Parameswaran Nair (463763)
Michael Kobor (3470795)
Tillie-Louise Hackett (92016)
Alan Knox (456628)

March 2018

Figure S1. (.EPS): CpG methylation variation in parenchymal fibroblasts in COPD samples. A) Plot of ...

DNA Methylome Alterations are Associated with Airway Macrophage Differentiation and Phenotype During Lung Fibrosis.

McErlean, P
Bell, CG
Hewitt, RJ
Busharat, Z
Ogger, PP
Ghai, P
Albers, GJ
Calamita, E
Kingston, S
Molyneaux, PL
Beck, S
Lloyd, CM
Maher, TM
Byrne, AJ

July 2021

RATIONALE: Airway macrophages (AMs) are key regulators of the lung environment and are implicated in...

Additional file 5: of Genome-wide analysis of DNA methylation in bronchial washings

Sang-Won Um (535627)
Yujin Kim (483088)
Bo Lee (3463586)
Dongho Kim (29790)
Kyung-Jong Lee (5237399)
Hong Kim (101826)
Joungho Han (483091)
Hojoong Kim (535625)
Young Shim (3463580)
Duk-Hwan Kim (483093)

May 2018

Table S3. The correlation between pack-years of smoking and DNA methylation in 53 control groups. (D...

Additional file 1: of Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Youdinghuan Chen (6067190)
David Armstrong (109098)
Lucas Salas (3711079)
Haley Hazlett (4055179)
Amanda Nymon (3203016)
John Dessaint (6067199)
Daniel Aridgides (380663)
Diane Mellinger (6067205)
Xiaoying Liu (192486)
Brock Christensen (3472082)
Alix Ashare (2549707)

December 2018

Table S1. Top hypo- and hyper-methylated CpGs in CF that are associated with known genes. (DOCX 17Â ...

Additional file 3: of Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Youdinghuan Chen (6067190)
David Armstrong (109098)
Lucas Salas (3711079)
Haley Hazlett (4055179)
Amanda Nymon (3203016)
John Dessaint (6067199)
Daniel Aridgides (380663)
Diane Mellinger (6067205)
Xiaoying Liu (192486)
Brock Christensen (3472082)
Alix Ashare (2549707)

December 2018

Table S2. Targeted next-generation bisulfite sequencing of EPIC identified genes. (DOCX 15Â kb

Additional file 2: of Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Youdinghuan Chen (6067190)
David Armstrong (109098)
Lucas Salas (3711079)
Haley Hazlett (4055179)
Amanda Nymon (3203016)
John Dessaint (6067199)
Daniel Aridgides (380663)
Diane Mellinger (6067205)
Xiaoying Liu (192486)
Brock Christensen (3472082)
Alix Ashare (2549707)

December 2018

Figure S1. Human leukocyte-specific protein-1 (LSP1) gene targeted next-generation sequencing (tNGS)...

Additional file 2: Figure S2. of DNA methylation at modifier genes of lung disease severity is altered in cystic fibrosis

Milena Magalhães (3747409)
Isabelle Rivals (144406)
Mireille Claustres (10836)
Jessica Varilh (396831)
Mélodie Thomasset (3747403)
Anne Bergougnoux (3747412)
Laurent Mely (3747415)
Sylvie Leroy (175152)
Harriet Corvol (313303)
Loïc Guillot (41929)
Marlène Murris (3747406)
Emmanuelle Beyne (72051)
Davide Caimmi (3747400)
Isabelle Vachier (3526700)
Raphaël Chiron (321612)
Albertina De Sario (222714)

February 2017

DNA methylation distribution at 14 analyzed genes in CF and control samples. (PDF 212 kb

Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Youdinghuan Chen
David A. Armstrong
Lucas A. Salas
Haley F. Hazlett
Amanda B. Nymon
John A. Dessaint
Daniel S. Aridgides
Diane L. Mellinger
Xiaoying Liu
Brock C. Christensen
Alix Ashare

December 2018

Abstract Background Lung macrophages are major participants in the pulmonary innate immune response....

Additional file 3: Figure S2. of Genome-wide DNA methylation profiling reveals novel epigenetic signatures in squamous cell lung cancer

Yuan-Xiang Shi (4614283)
Ying Wang (11406)
Xi Li (19208)
Wei Zhang (405)
Hong-Hao Zhou (156418)
Ji-Ye Yin (156407)
Zhao-Qian Liu (156422)

November 2017

Genomic context of CpG methylation. (A) The overall distribution of methylation sites in tumor versu...

Additional file 1: of Genome-wide DNA methylation profiling in whole blood reveals epigenetic signatures associated with migraine

Zachary Gerring (4787301)
Allan McRae (3400103)
Grant Montgomery (16569)
Dale Nyholt (4787298)

January 2018

Differentially methylated regions identified by a sliding window analysis. This file contains the ge...

Additional file 9: Table S8. of DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases

Symen Ligthart (701678)
Carola Marzi (236979)
Stella Aslibekyan (123439)
Michael Mendelson (2697424)
Karen Conneely (3448694)
Toshiko Tanaka (174638)
Elena Colicino (3503048)
Lindsay Waite (3503021)
Roby Joehanes (560601)
Weihua Guan (345071)
Jennifer Brody (174723)
Cathy Elks (3503054)
Riccardo Marioni (669892)
Min Jhun (3503015)
Golareh Agha (3503030)
Jan Bressler (248795)
Cavin Ward-Caviness (3503057)
Brian Chen (149932)
Tianxiao Huan (599733)
Kelly Bakulski (3503063)
Elias Salfati (3503045)
Giovanni Fiorito (136942)
Simone Wahl (112749)
Katharina Schramm (528479)
Jin Sha (847984)
Dena Hernandez (215322)
Allan Just (3448679)
Jennifer Smith (172056)
Nona Sotoodehnia (143373)
Luke Pilling (3503024)
James Pankow (160621)
Phil Tsao (3503066)
Chunyu Liu (9855)
Wei Zhao (14321)
Simonetta Guarrera (136940)
Vasiliki Michopoulos (3503051)
Alicia Smith (3448658)
Marjolein Peters (3503033)
David Melzer (202058)
Pantel Vokonas (587472)
Myriam Fornage (45591)
Holger Prokisch (26590)
Joshua Bis (711982)
Audrey Chu (3503069)
Christian Herder (44905)
Harald Grallert (72666)
Chen Yao (137375)
Sonia Shah (142603)
Allan McRae (3400103)
Honghuang Lin (560598)
Steve Horvath (28847)
Daniele Fallin (3503039)
Albert Hofman (107303)
Nicholas Wareham (153226)
Kerri Wiggins (3503018)
Andrew Feinberg (242567)
John Starr (231855)
Peter Visscher (3400094)
Joanne Murabito (3503036)
Sharon Kardia (3503060)
Devin Absher (217357)
Elisabeth Binder (3448661)
Andrew Singleton (23294)
Stefania Bandinelli (150002)
Annette Peters (62601)
Melanie Waldenberger (236985)
Giuseppe Matullo (136983)
Joel Schwartz (18324)
Ellen Demerath (198657)
AndrĂŠ Uitterlinden (3404267)
Joyce van Meurs (3404240)
Oscar Franco (2885594)
Yii-Der Chen (3503075)
Daniel Levy (51573)
Stephen Turner (3503027)
Ian Deary (489588)
Kerry Ressler (3503072)
JosĂŠe Dupuis (3503084)
Luigi Ferrucci (150038)
Ken Ong (448067)
Themistocles Assimes (746456)
Eric Boerwinkle (36288)
Wolfgang Koenig (26222)
Donna Arnett (192289)
Andrea Baccarelli (36523)
Emelia Benjamin (3503042)
Abbas Dehghan (174878)

December 2016

Significant methylation-expression results and corresponding expression-CRP results for the replicat...

Additional file 1: of Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD

Rachel Clifford (4913317)
Nick Fishbane (517664)
Jamie Patel (4913314)
Julia MacIsaac (3575030)
Lisa McEwen (3968174)
Andrew Fisher (1673086)
Corry-Anke Brandsma (41865)
Parameswaran Nair (463763)
Michael Kobor (3470795)
Tillie-Louise Hackett (92016)
Alan Knox (456628)

March 2018

Table S1. (.MWD): DNA regions differentially methylated with COPD status in airway fibroblasts. Summ...

Additional file 2 of An epigenetic and transcriptomic signature of immune tolerance in human monocytes through multi-omics integration

Xanthe Brands (8802716)
Bastiaan W. Haak (8802719)
Augustijn M. Klarenbeek (8802722)
Joe Butler (4331395)
Fabrice Uhel (3682579)
Wanhai Qin (10515966)
Natasja A. Otto (8802725)
Marja E. Jakobs (11282828)
Daniël R. Faber (8802728)
René Lutter (3407615)
W. Joost Wiersinga (8802734)
Tom van der Poll (33907)
Brendon P. Scicluna (8802731)

August 2021

Additional file 2: Supplementary figures (Fig. S1 – S5). Fig. S1: Flow cytometry analysis of purifie...

Additional file 5: Table S4. of DNA methylation profiling in peripheral lung tissues of smokers and patients with COPD

Isaac Sundar (3927785)
Qiangzong Yin (3927788)
Brian Baier (517434)
Li Yan (107001)
Witold Mazur (2118115)
Dongmei Li (176178)
Martha Susiarjo (23984)
Irfan Rahman (333928)

April 2017

CpGs differentially methylated in lung DNA in relation to smokers vs. non-smokers (Pâ<â0.01). (C...

DNA methylome alterations are associated with airway macrophage differentiation and phenotype during lung fibrosis.

McErlean, P
Bell, CG
Hewitt, RJ
Busharat, Z
Ogger, PP
Ghai, P
Albers, GJ
Calamita, E
Kingston, S
Molyneaux, PL
Beck, S
Lloyd, CM
Maher, TM
Byrne, AJ

July 2021

Rationale: Airway macrophages (AMs) are key regulators of the lung environment and are implicated in...

Additional file 3: of Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD

Rachel Clifford (4913317)
Nick Fishbane (517664)
Jamie Patel (4913314)
Julia MacIsaac (3575030)
Lisa McEwen (3968174)
Andrew Fisher (1673086)
Corry-Anke Brandsma (41865)
Parameswaran Nair (463763)
Michael Kobor (3470795)
Tillie-Louise Hackett (92016)
Alan Knox (456628)

March 2018

Figure S1. (.EPS): CpG methylation variation in parenchymal fibroblasts in COPD samples. A) Plot of ...

DNA Methylome Alterations are Associated with Airway Macrophage Differentiation and Phenotype During Lung Fibrosis.

McErlean, P
Bell, CG
Hewitt, RJ
Busharat, Z
Ogger, PP
Ghai, P
Albers, GJ
Calamita, E
Kingston, S
Molyneaux, PL
Beck, S
Lloyd, CM
Maher, TM
Byrne, AJ

July 2021

RATIONALE: Airway macrophages (AMs) are key regulators of the lung environment and are implicated in...

Additional file 5: of Genome-wide analysis of DNA methylation in bronchial washings

Sang-Won Um (535627)
Yujin Kim (483088)
Bo Lee (3463586)
Dongho Kim (29790)
Kyung-Jong Lee (5237399)
Hong Kim (101826)
Joungho Han (483091)
Hojoong Kim (535625)
Young Shim (3463580)
Duk-Hwan Kim (483093)

May 2018

Table S3. The correlation between pack-years of smoking and DNA methylation in 53 control groups. (D...

Additional file 5: of Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Abstract

Extracted data

Additional file 5: of Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Abstract

Extracted data

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