Additional file 5: of Comparison of different cell type correction methods for genome-scale epigenetics studies

Additional file 5 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

Pellegrino-Coppola, Damiano
Claringbould, Annique
Stutvoet, Maartje
Boomsma, Dorret I.
Ikram, M. Arfan
Slagboom, P. Eline
Westra, Harm-Jan
Franke, Lude
Coppola, Damiano Pellegrino
Slagboom, Eline
Faculteit Medische Wetenschappen/UMCG
Stem Cell Aging Leukemia and Lymphoma (SALL)
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Arctic Centre, Univ. of Groningen
VU University Medical Center
Erasmus University Medical Center
Leiden University Medical Center
University Medical Center Groningen

January 2021

Additional file 5: Table S5. The number of total overlapping genes (upper part), the conservation of...

Additional file 2: Table S2. of Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold

Edmund Glass (3502202)
Mikhail Dozmorov (4630)

October 2016

An example of LRCDE and csSAM analysis results of simulated data with 18 samples per group. Target c...

Additional file 5: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

Yuanxin Xi (255031)
Jiejun Shi (400725)
Wenqian Li (300451)
Kaori Tanaka (2834345)
Kendra Allton (180697)
Dana Richardson (4865026)
Jing Li (10611)
Hector Franco (4865011)
Anusha Nagari (4865008)
Venkat Malladi (4865014)
Luis Coletta (4865020)
Melissa Simper (4865017)
Khandan Keyomarsi (174628)
Jianjun Shen (231389)
Mark Bedford (3834187)
Xiaobing Shi (534669)
Michelle Barton (1906375)
W. Kraus (5791901)
Wei Li (7081)
Sharon Dent (4865023)

February 2018

Figure S3. ChromHMM model of 15 chromtain states defined by all 8 histone modifications. (PDF 358Â k...

Additional file 4: of Comparison of different cell type correction methods for genome-scale epigenetics studies

Akhilesh Kaushal (3927674)
Hongmei Zhang (179574)
Wilfried Karmaus (51303)
Meredith Ray (3927671)
Mylin Torres (3927677)
Alicia Smith (3448658)
Shu-Li Wang (43203)

April 2017

Supplemental Material S4. Boxplots depicting the difference in proportions for six cell types across...

Additional file 1: of Comparison of different cell type correction methods for genome-scale epigenetics studies

Akhilesh Kaushal (3927674)
Hongmei Zhang (179574)
Wilfried Karmaus (51303)
Meredith Ray (3927671)
Mylin Torres (3927677)
Alicia Smith (3448658)
Shu-Li Wang (43203)

April 2017

Supplemental Material S1. Figure A. Pearson correlations between inorganic arsenic levels (in log10 ...

Additional file 5: of CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types

Bradlee Nelms (3441425)
Levi Waldron (103807)
Luis Barrera (3441443)
Andrew Weflen (3441437)
Jeremy Goettel (3441434)
Guoji Guo (3441431)
Robert Montgomery (3441428)
Marian Neutra (3441446)
David Breault (3441422)
Scott Snapper (3436577)
Stuart Orkin (235037)
Martha Bulyk (3441440)
Curtis Huttenhower (21159)
Wayne Lencer (205412)

September 2016

Robustness of CellMapper to bias in dataset composition. Samples were drawn from the Lukk et al. [28...

Additional file 1: of A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies

Andrew Teschendorff (95936)
Charles Breeze (3512645)
Shijie Zheng (3428939)
Stephan Beck (5246)

February 2017

Contains all Supplementary Figures and Supplementary Tables plus their captions: Figure S1. Clusteri...

Comparison of different cell type correction methods for genome-scale epigenetics studies

Kaushal, Akhilesh
Zhang, Hongmei
Karmaus, Wilfried J.J.
Ray, Meredith
Torres, Mylin A.
Smith, Alicia K.
Wang, Shu Li

April 2017

Background: Whole blood is frequently utilized in genome-wide association studies of DNA methylation...

Additional file 1: of Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

Francesco Iorio (408438)
Fiona Behan (5626649)
Emanuel Gonรงalves (5626652)
Shriram Bhosle (10114)
Elisabeth Chen (5626655)
Rebecca Shepherd (5626658)
Charlotte Beaver (5626661)
Rizwan Ansari (5626667)
Rachel Pooley (5626670)
Piers Wilkinson (5626673)
Sarah Harper (5226377)
Adam Butler (658177)
Euan Stronach (5626676)
Julio Saez-Rodriguez (25229)
Kosuke Yusa (3175638)
Mathew Garnett (408439)

August 2018

Table S1. Project Score cell lines included in the study with annotations and screening description....

Additional file 1 of Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL)

Devin Koestler (3472088)
Meaghan Jones (3075183)
Joseph Usset (3472085)
Brock Christensen (3472082)
Rondi Butler (2560969)
Michael Kobor (3470795)
John Wiencke (381875)
Karl Kelsey (3398846)

March 2016

Table S1. Summary of cell distribution measurements/cell mixture adjustment, among random sample of ...

Additional file 5: of A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation

Dirk Paul (3428945)
Allison Jones (184670)
Rob Sellar (3565928)
Neema Mayor (3565949)
Andrew Feber (3559562)
Amy Webster (3565940)
Neuza Afonso (3565946)
Ruhena Sergeant (273708)
Richard Szydlo (3565934)
Jane Apperley (3565931)
Martin Widschwendter (184711)
Stephen Mackinnon (510464)
Steven Marsh (3565937)
J. Madrigal (3565943)
Vardhman Rakyan (3191682)
Karl Peggs (594447)
Stephan Beck (5246)

December 2015

Estimation of differential leukocyte counts. For each sample, the composition of major leukocyte cel...

Additional file 1: of Epigenetically maintained SW13+ and SW13- subtypes have different oncogenic potential and convert with HDAC1 inhibition

McKale Davis (3449099)
Juliane Daggett (3449111)
Agnes Pascual (3449105)
Jessica Lam (3449108)
Kathryn Leyva (3449102)
Kimbal Cooper (3449093)
Elizabeth Hull (3449096)

May 2016

Human Epigenetic Chromatin Modification Enzymes and Epigenetic Chromatin Remodeling Factors RT2 Prof...

Additional file 1 of Genome-wide analysis of epigenetic dynamics across human developmental stages and tissues

Xia Zhang (41398)
Yanglan Gan (6574184)
Guobing Zou (3602486)
Jihong Guan (3602441)
Shuigeng Zhou (181515)

April 2019

Figure S1. Performance comparisons for primary tissues among our method DiffEM, IOD and QDMR for eac...

Additional file 5: of Systematic evaluation of signal-to-noise ratio in variant detection from single cell genome multiple displacement amplification and exome sequencing

Anita Simonsen (5755358)
Marcus Hansen (5755361)
Eigil Kjeldsen (587943)
Peter MĂ¸ller (5755364)
Johnny HindkjĂŚr (5755367)
Peter Hokland (5755370)
Anni Aggerholm (5755373)

September 2018

Figure S4. Deterioration of allele frequencies (AF) and copy number signals by decreased cell input....

Additional file 5: Figure S4. of One-step genetic correction of hemoglobin E/beta-thalassemia patient-derived iPSCs by the CRISPR/Cas9 system

Methichit Wattanapanitch (627973)
Nattaya Damkham (4889524)
Ponthip Potirat (4889521)
Kongtana Trakarnsanga (597732)
Montira Janan (4889527)
Yaowalak U-pratya (627977)
Pakpoom Kheolamai (627979)
Nuttha Klincumhom (627974)
Surapol Issaragrisil (627981)

February 2018

Showing gene expression profile ofÂ the differentiated cells. (a) qRT-PCR analysis of hematopoietic ...

Additional file 5 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

Pellegrino-Coppola, Damiano
Claringbould, Annique
Stutvoet, Maartje
Boomsma, Dorret I.
Ikram, M. Arfan
Slagboom, P. Eline
Westra, Harm-Jan
Franke, Lude
Coppola, Damiano Pellegrino
Slagboom, Eline
Faculteit Medische Wetenschappen/UMCG
Stem Cell Aging Leukemia and Lymphoma (SALL)
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Arctic Centre, Univ. of Groningen
VU University Medical Center
Erasmus University Medical Center
Leiden University Medical Center
University Medical Center Groningen

January 2021

Additional file 5: Table S5. The number of total overlapping genes (upper part), the conservation of...

Additional file 2: Table S2. of Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold

Edmund Glass (3502202)
Mikhail Dozmorov (4630)

October 2016

An example of LRCDE and csSAM analysis results of simulated data with 18 samples per group. Target c...

Additional file 5: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

Yuanxin Xi (255031)
Jiejun Shi (400725)
Wenqian Li (300451)
Kaori Tanaka (2834345)
Kendra Allton (180697)
Dana Richardson (4865026)
Jing Li (10611)
Hector Franco (4865011)
Anusha Nagari (4865008)
Venkat Malladi (4865014)
Luis Coletta (4865020)
Melissa Simper (4865017)
Khandan Keyomarsi (174628)
Jianjun Shen (231389)
Mark Bedford (3834187)
Xiaobing Shi (534669)
Michelle Barton (1906375)
W. Kraus (5791901)
Wei Li (7081)
Sharon Dent (4865023)

February 2018

Figure S3. ChromHMM model of 15 chromtain states defined by all 8 histone modifications. (PDF 358Â k...

Additional file 4: of Comparison of different cell type correction methods for genome-scale epigenetics studies

Akhilesh Kaushal (3927674)
Hongmei Zhang (179574)
Wilfried Karmaus (51303)
Meredith Ray (3927671)
Mylin Torres (3927677)
Alicia Smith (3448658)
Shu-Li Wang (43203)

April 2017

Supplemental Material S4. Boxplots depicting the difference in proportions for six cell types across...

Additional file 1: of Comparison of different cell type correction methods for genome-scale epigenetics studies

Akhilesh Kaushal (3927674)
Hongmei Zhang (179574)
Wilfried Karmaus (51303)
Meredith Ray (3927671)
Mylin Torres (3927677)
Alicia Smith (3448658)
Shu-Li Wang (43203)

April 2017

Supplemental Material S1. Figure A. Pearson correlations between inorganic arsenic levels (in log10 ...

Additional file 5: of CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types

Bradlee Nelms (3441425)
Levi Waldron (103807)
Luis Barrera (3441443)
Andrew Weflen (3441437)
Jeremy Goettel (3441434)
Guoji Guo (3441431)
Robert Montgomery (3441428)
Marian Neutra (3441446)
David Breault (3441422)
Scott Snapper (3436577)
Stuart Orkin (235037)
Martha Bulyk (3441440)
Curtis Huttenhower (21159)
Wayne Lencer (205412)

September 2016

Robustness of CellMapper to bias in dataset composition. Samples were drawn from the Lukk et al. [28...

Additional file 1: of A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies

Andrew Teschendorff (95936)
Charles Breeze (3512645)
Shijie Zheng (3428939)
Stephan Beck (5246)

February 2017

Contains all Supplementary Figures and Supplementary Tables plus their captions: Figure S1. Clusteri...

Comparison of different cell type correction methods for genome-scale epigenetics studies

Kaushal, Akhilesh
Zhang, Hongmei
Karmaus, Wilfried J.J.
Ray, Meredith
Torres, Mylin A.
Smith, Alicia K.
Wang, Shu Li

April 2017

Background: Whole blood is frequently utilized in genome-wide association studies of DNA methylation...

Additional file 1: of Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

Francesco Iorio (408438)
Fiona Behan (5626649)
Emanuel Gonรงalves (5626652)
Shriram Bhosle (10114)
Elisabeth Chen (5626655)
Rebecca Shepherd (5626658)
Charlotte Beaver (5626661)
Rizwan Ansari (5626667)
Rachel Pooley (5626670)
Piers Wilkinson (5626673)
Sarah Harper (5226377)
Adam Butler (658177)
Euan Stronach (5626676)
Julio Saez-Rodriguez (25229)
Kosuke Yusa (3175638)
Mathew Garnett (408439)

August 2018

Table S1. Project Score cell lines included in the study with annotations and screening description....

Additional file 1 of Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL)

Devin Koestler (3472088)
Meaghan Jones (3075183)
Joseph Usset (3472085)
Brock Christensen (3472082)
Rondi Butler (2560969)
Michael Kobor (3470795)
John Wiencke (381875)
Karl Kelsey (3398846)

March 2016

Table S1. Summary of cell distribution measurements/cell mixture adjustment, among random sample of ...

Additional file 5: of A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation

Dirk Paul (3428945)
Allison Jones (184670)
Rob Sellar (3565928)
Neema Mayor (3565949)
Andrew Feber (3559562)
Amy Webster (3565940)
Neuza Afonso (3565946)
Ruhena Sergeant (273708)
Richard Szydlo (3565934)
Jane Apperley (3565931)
Martin Widschwendter (184711)
Stephen Mackinnon (510464)
Steven Marsh (3565937)
J. Madrigal (3565943)
Vardhman Rakyan (3191682)
Karl Peggs (594447)
Stephan Beck (5246)

December 2015

Estimation of differential leukocyte counts. For each sample, the composition of major leukocyte cel...

Additional file 1: of Epigenetically maintained SW13+ and SW13- subtypes have different oncogenic potential and convert with HDAC1 inhibition

McKale Davis (3449099)
Juliane Daggett (3449111)
Agnes Pascual (3449105)
Jessica Lam (3449108)
Kathryn Leyva (3449102)
Kimbal Cooper (3449093)
Elizabeth Hull (3449096)

May 2016

Human Epigenetic Chromatin Modification Enzymes and Epigenetic Chromatin Remodeling Factors RT2 Prof...

Additional file 1 of Genome-wide analysis of epigenetic dynamics across human developmental stages and tissues

Xia Zhang (41398)
Yanglan Gan (6574184)
Guobing Zou (3602486)
Jihong Guan (3602441)
Shuigeng Zhou (181515)

April 2019

Figure S1. Performance comparisons for primary tissues among our method DiffEM, IOD and QDMR for eac...

Additional file 5: of Systematic evaluation of signal-to-noise ratio in variant detection from single cell genome multiple displacement amplification and exome sequencing

Anita Simonsen (5755358)
Marcus Hansen (5755361)
Eigil Kjeldsen (587943)
Peter MĂ¸ller (5755364)
Johnny HindkjĂŚr (5755367)
Peter Hokland (5755370)
Anni Aggerholm (5755373)

September 2018

Figure S4. Deterioration of allele frequencies (AF) and copy number signals by decreased cell input....

Additional file 5: Figure S4. of One-step genetic correction of hemoglobin E/beta-thalassemia patient-derived iPSCs by the CRISPR/Cas9 system

Methichit Wattanapanitch (627973)
Nattaya Damkham (4889524)
Ponthip Potirat (4889521)
Kongtana Trakarnsanga (597732)
Montira Janan (4889527)
Yaowalak U-pratya (627977)
Pakpoom Kheolamai (627979)
Nuttha Klincumhom (627974)
Surapol Issaragrisil (627981)

February 2018

Showing gene expression profile ofÂ the differentiated cells. (a) qRT-PCR analysis of hematopoietic ...

Additional file 5 of Correction for both common and rare cell types in blood is important to identify genes that correlate with age

Pellegrino-Coppola, Damiano
Claringbould, Annique
Stutvoet, Maartje
Boomsma, Dorret I.
Ikram, M. Arfan
Slagboom, P. Eline
Westra, Harm-Jan
Franke, Lude
Coppola, Damiano Pellegrino
Slagboom, Eline
Faculteit Medische Wetenschappen/UMCG
Stem Cell Aging Leukemia and Lymphoma (SALL)
Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)
Arctic Centre, Univ. of Groningen
VU University Medical Center
Erasmus University Medical Center
Leiden University Medical Center
University Medical Center Groningen

January 2021

Additional file 5: Table S5. The number of total overlapping genes (upper part), the conservation of...

Additional file 2: Table S2. of Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold

Edmund Glass (3502202)
Mikhail Dozmorov (4630)

October 2016

An example of LRCDE and csSAM analysis results of simulated data with 18 samples per group. Target c...

Additional file 5: of Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

Yuanxin Xi (255031)
Jiejun Shi (400725)
Wenqian Li (300451)
Kaori Tanaka (2834345)
Kendra Allton (180697)
Dana Richardson (4865026)
Jing Li (10611)
Hector Franco (4865011)
Anusha Nagari (4865008)
Venkat Malladi (4865014)
Luis Coletta (4865020)
Melissa Simper (4865017)
Khandan Keyomarsi (174628)
Jianjun Shen (231389)
Mark Bedford (3834187)
Xiaobing Shi (534669)
Michelle Barton (1906375)
W. Kraus (5791901)
Wei Li (7081)
Sharon Dent (4865023)

February 2018

Figure S3. ChromHMM model of 15 chromtain states defined by all 8 histone modifications. (PDF 358Â k...

Additional file 5: of Comparison of different cell type correction methods for genome-scale epigenetics studies

Abstract

Extracted data

Additional file 5: of Comparison of different cell type correction methods for genome-scale epigenetics studies

Abstract

Extracted data

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