Additional file 2: of Proteomic profiling identifies specific histone species associated with leukemic and cancer cells

Additional file 11: 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

Table S8. Significant pathways of subtype gene signatures of active transcription states and active ...

Additional file 3: Dataset S2. of PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples

Roberta Noberini (192067)
RĂŠmi LonguespĂŠe (3858958)
Cristina Richichi (4238719)
Giancarlo Pruneri (384238)
Mark Kriegsmann (3485276)
Giuliana Pelicci (190861)
Tiziana Bonaldi (35979)

July 2017

Dataset containing the measured AUCs and L/H ratios for the breast cancer samples shown in Figs.Â 3,...

Additional file 1: Figure S1. of Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer

Marsela Braunstein (3440615)
Linda Liao (3440618)
Nicola Lyttle (3440624)
Nazleen Lobo (623561)
Karen Taylor (2317915)
Paul Krzyzanowski (3440609)
Irina Kalatskaya (3440600)
Cindy Yao (3440612)
Lincoln Stein (14330)
Paul Boutros (196570)
Christopher Twelves (3440627)
Richard Marcellus (2554267)
John Bartlett (602286)
Melanie Spears (3440621)

February 2016

Clinical trial BR9601 information. (a) Schematic representation. (b) Patient information. Figure S2....

Additional file 1. of Proteomic profiling identifies specific histone species associated with leukemic and cancer cells

Rajbir Singh (451210)
Sean Harshman (3498065)
Amy Ruppert (3498059)
Amir Mortazavi (1939456)
David Lucas (3486539)
Jennifer Thomas-Ahner (3498062)
Steven Clinton (3498056)
John Byrd (28558)
Michael Freitas (3460514)
Mark Parthun (3460520)

August 2015

12 tables listing all of the core histone variants and their molecular weights. Additional tables li...

Additional file 1: 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 S1. Enrichment of histone modification ChIP-seq signals pooled from all sampled in (A) transc...

Additional file 2: of The hyper-activation of transcriptional enhancers in breast cancer

Qing-Lan Li (1344414)
Dan-Ya Wang (6456284)
Lin-Gao Ju (6456287)
Jie Yao (1440151)
Chuan Gao (38049)
Pin-Ji Lei (681939)
Lian-Yun Li (681943)
Xiao-Lu Zhao (6456290)
Min Wu (41570)

March 2019

Table S1. List of the relative abundance of all histone peptides. Table S2. List of the relative abu...

Additional file 18: 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

Table S3. Emission probability and transition probability of Chromatin States defined by ChromHMM. (...

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 8: 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 S5. Spearman correlation of H3K36me3 occupancy and gene expression levels in all samples. (PD...

Additional file 1: of The hyper-activation of transcriptional enhancers in breast cancer

Qing-Lan Li (1344414)
Dan-Ya Wang (6456284)
Lin-Gao Ju (6456287)
Jie Yao (1440151)
Chuan Gao (38049)
Pin-Ji Lei (681939)
Lian-Yun Li (681943)
Xiao-Lu Zhao (6456290)
Min Wu (41570)

March 2019

Figure S1. Multiple modifications on two peptides of histone H3 and H4. Figure S2. The proteomic pat...

Additional file 1: of Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma

Luis Nagai (6492632)
Sung-Joon Park (548075)
Kenta Nakai (408)

March 2019

This file includes: detailed information from data used, including statistical information of reads ...

Additional file 4: 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 S2. (A) Clustering of chromatin states model learned on individual cells showing same enrichm...

Additional file 9: 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

Table S4. List of genes with subtype specific active transcription states. (XLS 44Â kb

Additional file 7: 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

Table S5. List of genes with subtype specific active enhancer states. (XLS 212Â kb

Additional file 1: of Discovery of a diagnostic biomarker for colon cancer through proteomic profiling of small extracellular vesicles

Chan-Hyeong Lee (5759486)
Eun-Ju Im (3772540)
Pyong-Gon Moon (3772543)
Moon-Chang Baek (267704)

November 2018

Table S1. Protein list of small-EVs from HCT-116 and HT-29 CC cell lines. (XLSX 45 kb

Additional file 11: 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

Table S8. Significant pathways of subtype gene signatures of active transcription states and active ...

Additional file 3: Dataset S2. of PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples

Roberta Noberini (192067)
RĂŠmi LonguespĂŠe (3858958)
Cristina Richichi (4238719)
Giancarlo Pruneri (384238)
Mark Kriegsmann (3485276)
Giuliana Pelicci (190861)
Tiziana Bonaldi (35979)

July 2017

Dataset containing the measured AUCs and L/H ratios for the breast cancer samples shown in Figs.Â 3,...

Additional file 1: Figure S1. of Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer

Marsela Braunstein (3440615)
Linda Liao (3440618)
Nicola Lyttle (3440624)
Nazleen Lobo (623561)
Karen Taylor (2317915)
Paul Krzyzanowski (3440609)
Irina Kalatskaya (3440600)
Cindy Yao (3440612)
Lincoln Stein (14330)
Paul Boutros (196570)
Christopher Twelves (3440627)
Richard Marcellus (2554267)
John Bartlett (602286)
Melanie Spears (3440621)

February 2016

Clinical trial BR9601 information. (a) Schematic representation. (b) Patient information. Figure S2....

Additional file 1. of Proteomic profiling identifies specific histone species associated with leukemic and cancer cells

Rajbir Singh (451210)
Sean Harshman (3498065)
Amy Ruppert (3498059)
Amir Mortazavi (1939456)
David Lucas (3486539)
Jennifer Thomas-Ahner (3498062)
Steven Clinton (3498056)
John Byrd (28558)
Michael Freitas (3460514)
Mark Parthun (3460520)

August 2015

12 tables listing all of the core histone variants and their molecular weights. Additional tables li...

Additional file 1: 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 S1. Enrichment of histone modification ChIP-seq signals pooled from all sampled in (A) transc...

Additional file 2: of The hyper-activation of transcriptional enhancers in breast cancer

Qing-Lan Li (1344414)
Dan-Ya Wang (6456284)
Lin-Gao Ju (6456287)
Jie Yao (1440151)
Chuan Gao (38049)
Pin-Ji Lei (681939)
Lian-Yun Li (681943)
Xiao-Lu Zhao (6456290)
Min Wu (41570)

March 2019

Table S1. List of the relative abundance of all histone peptides. Table S2. List of the relative abu...

Additional file 18: 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

Table S3. Emission probability and transition probability of Chromatin States defined by ChromHMM. (...

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 8: 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 S5. Spearman correlation of H3K36me3 occupancy and gene expression levels in all samples. (PD...

Additional file 1: of The hyper-activation of transcriptional enhancers in breast cancer

Qing-Lan Li (1344414)
Dan-Ya Wang (6456284)
Lin-Gao Ju (6456287)
Jie Yao (1440151)
Chuan Gao (38049)
Pin-Ji Lei (681939)
Lian-Yun Li (681943)
Xiao-Lu Zhao (6456290)
Min Wu (41570)

March 2019

Figure S1. Multiple modifications on two peptides of histone H3 and H4. Figure S2. The proteomic pat...

Additional file 1: of Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma

Luis Nagai (6492632)
Sung-Joon Park (548075)
Kenta Nakai (408)

March 2019

This file includes: detailed information from data used, including statistical information of reads ...

Additional file 4: 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 S2. (A) Clustering of chromatin states model learned on individual cells showing same enrichm...

Additional file 9: 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

Table S4. List of genes with subtype specific active transcription states. (XLS 44Â kb

Additional file 7: 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

Table S5. List of genes with subtype specific active enhancer states. (XLS 212Â kb

Additional file 1: of Discovery of a diagnostic biomarker for colon cancer through proteomic profiling of small extracellular vesicles

Chan-Hyeong Lee (5759486)
Eun-Ju Im (3772540)
Pyong-Gon Moon (3772543)
Moon-Chang Baek (267704)

November 2018

Table S1. Protein list of small-EVs from HCT-116 and HT-29 CC cell lines. (XLSX 45 kb

Additional file 11: 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

Table S8. Significant pathways of subtype gene signatures of active transcription states and active ...

Additional file 3: Dataset S2. of PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples

Roberta Noberini (192067)
RĂŠmi LonguespĂŠe (3858958)
Cristina Richichi (4238719)
Giancarlo Pruneri (384238)
Mark Kriegsmann (3485276)
Giuliana Pelicci (190861)
Tiziana Bonaldi (35979)

July 2017

Dataset containing the measured AUCs and L/H ratios for the breast cancer samples shown in Figs.Â 3,...

Additional file 1: Figure S1. of Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer

Marsela Braunstein (3440615)
Linda Liao (3440618)
Nicola Lyttle (3440624)
Nazleen Lobo (623561)
Karen Taylor (2317915)
Paul Krzyzanowski (3440609)
Irina Kalatskaya (3440600)
Cindy Yao (3440612)
Lincoln Stein (14330)
Paul Boutros (196570)
Christopher Twelves (3440627)
Richard Marcellus (2554267)
John Bartlett (602286)
Melanie Spears (3440621)

February 2016

Clinical trial BR9601 information. (a) Schematic representation. (b) Patient information. Figure S2....

Additional file 2: of Proteomic profiling identifies specific histone species associated with leukemic and cancer cells

Abstract

Extracted data

Additional file 2: of Proteomic profiling identifies specific histone species associated with leukemic and cancer cells

Abstract

Extracted data

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