Additional file 7: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu
Shimeng Liu
Ping Yin
Serdar Bulun
Yang Dai

December 2018

Abstract Background DNA methylation of CpG dinucleotides is an essential epigenetic modification tha...

Additional file 1: Table S1. of Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

Stephan Busche (3465698)
Xiaojian Shao (3465695)
Maxime Caron (3465692)
Tony Kwan (232656)
Fiona Allum (3465704)
Warren Cheung (83908)
Bing Ge (42609)
Susan Westfall (392141)
Marie-Michelle Simon (3465701)
Amy Barrett (166784)
Jordana Bell (667256)
Mark McCarthy (157523)
Panos Deloukas (21564)
Mathieu Blanchette (5083)
Guillaume Bourque (123960)
Timothy Spector (348486)
Mark Lathrop (17971)
Tomi Pastinen (15737)
Elin Grundberg (116416)

December 2015

Sequencing statistics summary. Table S2. Genome feature association of filtered variant-removed CpGs...

MOESM1 of Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles

Toshiki Aiba (2466442)
Toshiyuki Saito (520509)
Akiko Hayashi (291910)
Shinji Sato (30480)
Harunobu Yunokawa (3827905)
Toru Maruyama (507201)
Wataru Fujibuchi (57484)
Hisaka Kurita (824603)
Chiharu Tohyama (111093)
Seiichiroh Ohsako (3827908)

March 2017

Additional file 1: Table S1. Oligonucleotides used for MSD-AFLP. Table S2. Locus-specific primers us...

Additional file5: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Figure S1. Comparison of the methods MEDIPS_normal and MEDIPS. Pearson correlation coefficient (PCC)...

Additional file 6: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Figure S2. Comparison of the methods MEDIPS_normal and MEDIPS. Spearman correlation coefficient (SCC...

Additional file 2: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Table S1. Pearson correlation coefficient of bin methylation level for the positive and negative DNA...

Additional file 4: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Table S3. Spearman correlation coefficient between the inferred bin methylation level and the RRBS d...

Additional file 3: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Table S2. Pearson correlation coefficient between the inferred bin methylation level and the RRBS da...

Additional file 1: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Correcting CpG density bias by the normal curve and Using WGBS data for validation. (DOCX 16 kb

Additional file 1: of BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues

Luli Zou (5269877)
Michael Erdos (3563438)
D. Leland Taylor (5105165)
Peter Chines (262585)
Arushi Varshney (5105171)
Stephen Parker (3563435)
Francis Collins (63274)
John Didion (3261849)

May 2018

Figure S1. Distribution of WGBS missingness across chromatin states, not normalized for total number...

Comparison of methylation level estimates for the bisulfite sequencing, HumanMethylation 450K and MeDIP-seq data.

Christine Clark (116413)
Priit Palta (116414)
Christopher J. Joyce (116415)
Carol Scott (67343)
Elin Grundberg (116416)
Panos Deloukas (21564)
Aarno Palotie (41342)
Alison J. Coffey (116421)

November 2012

<p>Data are shown for the 28 islands (associated with 36 genes) containing CpG sites that overlapped...

Additional file 5: of Comparing DNA methylation profiles in saliva and intestinal mucosa

Nerissa Hearn (6413723)
Aaron Coleman (6413726)
Vincent Ho (443227)
Christine Chiu (6413729)
Joanne Lind (3489548)

March 2019

Figure S3. Manhattan Plot. Manhattan plot of each CpG site plotted according to genomic position on ...

Additional file 2: Figure S1. of Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

Stephan Busche (3465698)
Xiaojian Shao (3465695)
Maxime Caron (3465692)
Tony Kwan (232656)
Fiona Allum (3465704)
Warren Cheung (83908)
Bing Ge (42609)
Susan Westfall (392141)
Marie-Michelle Simon (3465701)
Amy Barrett (166784)
Jordana Bell (667256)
Mark McCarthy (157523)
Panos Deloukas (21564)
Mathieu Blanchette (5083)
Guillaume Bourque (123960)
Timothy Spector (348486)
Mark Lathrop (17971)
Tomi Pastinen (15737)
Elin Grundberg (116416)

December 2015

Number of detected CpG-sites per mean genome coverage. Figure S2. Overall CpG-site methylation level...

Additional file 1: of DNA methylome profiling at single-base resolution through bisulfite sequencing of 5mC-immunoprecipitated DNA

Zhen Jia (192249)
Yueyi Shi (3900601)
Lei Zhang (38117)
Yipeng Ren (719203)
Tong Wang (87696)
Lejun Xing (4831500)
Baorong Zhang (445204)
Guolan Gao (522590)
Rongfa Bu (3900604)

February 2018

Table S1. No adverse effect of methylated AluI-linker on MeDIP enrichment. Table S2. Evidence of a d...

Additional file 3: of Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer

Simeng Gu (6438257)
Shujuan Lin (6169328)
Ding Ye (405963)
Sangni Qian (6438266)
Danjie Jiang (395701)
Xiaocong Zhang (6438269)
Qilong Li (5477081)
Jinhua Yang (2019088)
Xiaojiang Ying (538813)
Zhenjun Li (275953)
Mengling Tang (644955)
Jianbing Wang (5118731)
Mingjuan Jin (186609)
Kun Chen (131048)

March 2019

Figure S1. a Pearson correlation analysis between age and methylation level of MPPED2. b Pearson cor...

MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu
Shimeng Liu
Ping Yin
Serdar Bulun
Yang Dai

December 2018

Abstract Background DNA methylation of CpG dinucleotides is an essential epigenetic modification tha...

Additional file 1: Table S1. of Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

Stephan Busche (3465698)
Xiaojian Shao (3465695)
Maxime Caron (3465692)
Tony Kwan (232656)
Fiona Allum (3465704)
Warren Cheung (83908)
Bing Ge (42609)
Susan Westfall (392141)
Marie-Michelle Simon (3465701)
Amy Barrett (166784)
Jordana Bell (667256)
Mark McCarthy (157523)
Panos Deloukas (21564)
Mathieu Blanchette (5083)
Guillaume Bourque (123960)
Timothy Spector (348486)
Mark Lathrop (17971)
Tomi Pastinen (15737)
Elin Grundberg (116416)

December 2015

Sequencing statistics summary. Table S2. Genome feature association of filtered variant-removed CpGs...

MOESM1 of Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles

Toshiki Aiba (2466442)
Toshiyuki Saito (520509)
Akiko Hayashi (291910)
Shinji Sato (30480)
Harunobu Yunokawa (3827905)
Toru Maruyama (507201)
Wataru Fujibuchi (57484)
Hisaka Kurita (824603)
Chiharu Tohyama (111093)
Seiichiroh Ohsako (3827908)

March 2017

Additional file 1: Table S1. Oligonucleotides used for MSD-AFLP. Table S2. Locus-specific primers us...

Additional file5: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Figure S1. Comparison of the methods MEDIPS_normal and MEDIPS. Pearson correlation coefficient (PCC)...

Additional file 6: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Figure S2. Comparison of the methods MEDIPS_normal and MEDIPS. Spearman correlation coefficient (SCC...

Additional file 2: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Table S1. Pearson correlation coefficient of bin methylation level for the positive and negative DNA...

Additional file 4: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Table S3. Spearman correlation coefficient between the inferred bin methylation level and the RRBS d...

Additional file 3: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Table S2. Pearson correlation coefficient between the inferred bin methylation level and the RRBS da...

Additional file 1: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu (3134982)
Shimeng Liu (6112952)
Ping Yin (54021)
Serdar Bulun (6112955)
Yang Dai (36730)

December 2018

Correcting CpG density bias by the normal curve and Using WGBS data for validation. (DOCX 16 kb

Additional file 1: of BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues

Luli Zou (5269877)
Michael Erdos (3563438)
D. Leland Taylor (5105165)
Peter Chines (262585)
Arushi Varshney (5105171)
Stephen Parker (3563435)
Francis Collins (63274)
John Didion (3261849)

May 2018

Figure S1. Distribution of WGBS missingness across chromatin states, not normalized for total number...

Comparison of methylation level estimates for the bisulfite sequencing, HumanMethylation 450K and MeDIP-seq data.

Christine Clark (116413)
Priit Palta (116414)
Christopher J. Joyce (116415)
Carol Scott (67343)
Elin Grundberg (116416)
Panos Deloukas (21564)
Aarno Palotie (41342)
Alison J. Coffey (116421)

November 2012

<p>Data are shown for the 28 islands (associated with 36 genes) containing CpG sites that overlapped...

Additional file 5: of Comparing DNA methylation profiles in saliva and intestinal mucosa

Nerissa Hearn (6413723)
Aaron Coleman (6413726)
Vincent Ho (443227)
Christine Chiu (6413729)
Joanne Lind (3489548)

March 2019

Figure S3. Manhattan Plot. Manhattan plot of each CpG site plotted according to genomic position on ...

Additional file 2: Figure S1. of Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

Stephan Busche (3465698)
Xiaojian Shao (3465695)
Maxime Caron (3465692)
Tony Kwan (232656)
Fiona Allum (3465704)
Warren Cheung (83908)
Bing Ge (42609)
Susan Westfall (392141)
Marie-Michelle Simon (3465701)
Amy Barrett (166784)
Jordana Bell (667256)
Mark McCarthy (157523)
Panos Deloukas (21564)
Mathieu Blanchette (5083)
Guillaume Bourque (123960)
Timothy Spector (348486)
Mark Lathrop (17971)
Tomi Pastinen (15737)
Elin Grundberg (116416)

December 2015

Number of detected CpG-sites per mean genome coverage. Figure S2. Overall CpG-site methylation level...

Additional file 1: of DNA methylome profiling at single-base resolution through bisulfite sequencing of 5mC-immunoprecipitated DNA

Zhen Jia (192249)
Yueyi Shi (3900601)
Lei Zhang (38117)
Yipeng Ren (719203)
Tong Wang (87696)
Lejun Xing (4831500)
Baorong Zhang (445204)
Guolan Gao (522590)
Rongfa Bu (3900604)

February 2018

Table S1. No adverse effect of methylated AluI-linker on MeDIP enrichment. Table S2. Evidence of a d...

Additional file 3: of Genome-wide methylation profiling identified novel differentially hypermethylated biomarker MPPED2 in colorectal cancer

Simeng Gu (6438257)
Shujuan Lin (6169328)
Ding Ye (405963)
Sangni Qian (6438266)
Danjie Jiang (395701)
Xiaocong Zhang (6438269)
Qilong Li (5477081)
Jinhua Yang (2019088)
Xiaojiang Ying (538813)
Zhenjun Li (275953)
Mengling Tang (644955)
Jianbing Wang (5118731)
Mingjuan Jin (186609)
Kun Chen (131048)

March 2019

Figure S1. a Pearson correlation analysis between age and methylation level of MPPED2. b Pearson cor...

MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Jingting Xu
Shimeng Liu
Ping Yin
Serdar Bulun
Yang Dai

December 2018

Abstract Background DNA methylation of CpG dinucleotides is an essential epigenetic modification tha...

Additional file 1: Table S1. of Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

Stephan Busche (3465698)
Xiaojian Shao (3465695)
Maxime Caron (3465692)
Tony Kwan (232656)
Fiona Allum (3465704)
Warren Cheung (83908)
Bing Ge (42609)
Susan Westfall (392141)
Marie-Michelle Simon (3465701)
Amy Barrett (166784)
Jordana Bell (667256)
Mark McCarthy (157523)
Panos Deloukas (21564)
Mathieu Blanchette (5083)
Guillaume Bourque (123960)
Timothy Spector (348486)
Mark Lathrop (17971)
Tomi Pastinen (15737)
Elin Grundberg (116416)

December 2015

Sequencing statistics summary. Table S2. Genome feature association of filtered variant-removed CpGs...

MOESM1 of Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles

Toshiki Aiba (2466442)
Toshiyuki Saito (520509)
Akiko Hayashi (291910)
Shinji Sato (30480)
Harunobu Yunokawa (3827905)
Toru Maruyama (507201)
Wataru Fujibuchi (57484)
Hisaka Kurita (824603)
Chiharu Tohyama (111093)
Seiichiroh Ohsako (3827908)

March 2017

Additional file 1: Table S1. Oligonucleotides used for MSD-AFLP. Table S2. Locus-specific primers us...

Additional file 7: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Abstract

Extracted data

Additional file 7: of MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data

Abstract

Extracted data

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