Additional file 3: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

Publication date

November 2018

DOI

10.6084/m9.figshare.7313804.v1

Abstract

Table S2. RNA-seq expression profile of all genes analyzed (total genes 22548) in young, aged, and aged CASIN-treated HSCs. (XLSX 2254 kb

Extracted data

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Data Protection

Additional file 3: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

Open link

Publication date

November 2018

DOI

10.6084/m9.figshare.7313804.v1

Abstract

Table S2. RNA-seq expression profile of all genes analyzed (total genes 22548) in young, aged, and aged CASIN-treated HSCs. (XLSX 2254 kb

Extracted data

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 3: Table S3. of Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling

Anthony Zannas (3577409)
Janine Arloth (434022)
Tania Carrillo-Roa (3577415)
Stella Iurato (3448718)
Simone Röh (434023)
Kerry Ressler (3503072)
Charles Nemeroff (3577418)
Alicia Smith (3448658)
Bekh Bradley (3577412)
Christine Heim (722556)
Andreas Menke (418090)
Jennifer Lange (3577421)
Tanja Brückl (418088)
Marcus Ising (195804)
Naomi Wray (3449882)
Angelika Erhardt (263710)
Elisabeth Binder (3448661)
Divya Mehta (138812)

December 2015

WebGestalt Disease enrichment analysis of the set of unique DEX-regulated genes (n = 139) with TSS n...

Additional file 4: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Table S3. Comparisons with three different stringency levels (no false discovery rate adjustment (no...

Additional file 2: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Table S1. 118 common genes that presented with differential binding of H4K16ac in young and aged CAS...

Additional file 13: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S9. 3D distribution of LaminA/C (green) in CASIN-treated aged HSCs. Nucleus is stained with DA...

Additional file 7: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S3. 3D distribution of chromosome 11 (red) in CASIN-treated aged HSCs. Nucleus is stained with...

Additional file 9: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S5. 3D distribution of H4K16ac (green) and chromosome 11 (red) in aged HSCs. Nucleus is staine...

Additional file 12: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S8. 3D distribution of LaminA/C (green) in aged HSCs. Nucleus is stained with DAPI (blue). (AV...

Additional file 6: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S2. 3D distribution of chromosome 11 (red) in aged HSCs. Nucleus is stained with DAPI (blue). ...

Additional file 8: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S4. 3D distribution of H4K16ac (green) and chromosome 11 (red) in young HSCs. Nucleus is stain...

Additional file 11: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S7. 3D distribution of LaminA/C (green) in young HSCs. Nucleus is stained with DAPI (blue). (A...

Additional file 5: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S1. 3D distribution of chromosome 11 (red) in young HSCs. Nucleus is stained with DAPI (blue)....

Additional file 2: Table S1. of Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability

David Nelson (302089)
Farah Jaber-Hijazi (3414056)
John Cole (392281)
Neil Robertson (25148)
Jeffrey Pawlikowski (105247)
Kevin Norris (3414062)
Steven Criscione (3414050)
Nikolay Pchelintsev (3414053)
Desiree Piscitello (3414080)
Nicholas Stong (3414074)
Taranjit Rai (3414059)
Tony McBryan (3414077)
Gabriel Otte (3414065)
Colin Nixon (589084)
William Clark (775696)
Harold Riethman (45358)
Hong Wu (105254)
Gunnar Schotta (116394)
Benjamin Garcia (3406175)
Nicola Neretti (47217)
Duncan Baird (349206)
Shelley Berger (3414068)
Peter Adams (3414071)

July 2016

Descriptive statistics for H4K20me3, histone H4, and input DNA ChIP sequencing reads from proliferat...

Epigenomic Profiling of Young and Aged HSCs Reveals Concerted Changes during Aging that Reinforce Self-Renewal

Sun, Deqiang
Luo, Min
Jeong, Mira
Rodriguez, Benjamin
Xia, Zheng
Hannah, Rebecca
Wang, Hui
Le, Thuc
Faull, Kym F.
Chen, Rui
Gu, Hongcang
Bock, Christoph
Meissner, Alexander
Göttgens, Berthold
Darlington, Gretchen J.
Li, Wei
Goodell, Margaret A.

May 2014

SummaryTo investigate the cell-intrinsic aging mechanisms that erode the function of somatic stem ce...

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 3: Table S3. of Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling

Anthony Zannas (3577409)
Janine Arloth (434022)
Tania Carrillo-Roa (3577415)
Stella Iurato (3448718)
Simone Röh (434023)
Kerry Ressler (3503072)
Charles Nemeroff (3577418)
Alicia Smith (3448658)
Bekh Bradley (3577412)
Christine Heim (722556)
Andreas Menke (418090)
Jennifer Lange (3577421)
Tanja Brückl (418088)
Marcus Ising (195804)
Naomi Wray (3449882)
Angelika Erhardt (263710)
Elisabeth Binder (3448661)
Divya Mehta (138812)

December 2015

WebGestalt Disease enrichment analysis of the set of unique DEX-regulated genes (n = 139) with TSS n...

Additional file 4: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Table S3. Comparisons with three different stringency levels (no false discovery rate adjustment (no...

Additional file 2: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Table S1. 118 common genes that presented with differential binding of H4K16ac in young and aged CAS...

Additional file 13: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S9. 3D distribution of LaminA/C (green) in CASIN-treated aged HSCs. Nucleus is stained with DA...

Additional file 7: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S3. 3D distribution of chromosome 11 (red) in CASIN-treated aged HSCs. Nucleus is stained with...

Additional file 9: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S5. 3D distribution of H4K16ac (green) and chromosome 11 (red) in aged HSCs. Nucleus is staine...

Additional file 12: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S8. 3D distribution of LaminA/C (green) in aged HSCs. Nucleus is stained with DAPI (blue). (AV...

Additional file 6: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S2. 3D distribution of chromosome 11 (red) in aged HSCs. Nucleus is stained with DAPI (blue). ...

Additional file 8: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S4. 3D distribution of H4K16ac (green) and chromosome 11 (red) in young HSCs. Nucleus is stain...

Additional file 11: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S7. 3D distribution of LaminA/C (green) in young HSCs. Nucleus is stained with DAPI (blue). (A...

Additional file 5: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Ani Grigoryan (5944232)
Novella Guidi (5944235)
Katharina Senger (144682)
Thomas Liehr (484)
Karin Soller (5774207)
Gina Marka (5774204)
Angelika Vollmer (3953435)
Yolanda Markaki (3502454)
Heinrich Leonhardt (18589)
Christian Buske (3722989)
Daniel Lipka (3512798)
Christoph Plass (14626)
Yi Zheng (113896)
Medhanie Mulaw (5944241)
Hartmut Geiger (144685)
Maria Florian (629873)

November 2018

Video S1. 3D distribution of chromosome 11 (red) in young HSCs. Nucleus is stained with DAPI (blue)....

David Nelson (302089)
Farah Jaber-Hijazi (3414056)
John Cole (392281)
Neil Robertson (25148)
Jeffrey Pawlikowski (105247)
Kevin Norris (3414062)
Steven Criscione (3414050)
Nikolay Pchelintsev (3414053)
Desiree Piscitello (3414080)
Nicholas Stong (3414074)
Taranjit Rai (3414059)
Tony McBryan (3414077)
Gabriel Otte (3414065)
Colin Nixon (589084)
William Clark (775696)
Harold Riethman (45358)
Hong Wu (105254)
Gunnar Schotta (116394)
Benjamin Garcia (3406175)
Nicola Neretti (47217)
Duncan Baird (349206)
Shelley Berger (3414068)
Peter Adams (3414071)

July 2016

Descriptive statistics for H4K20me3, histone H4, and input DNA ChIP sequencing reads from proliferat...

Epigenomic Profiling of Young and Aged HSCs Reveals Concerted Changes during Aging that Reinforce Self-Renewal

Sun, Deqiang
Luo, Min
Jeong, Mira
Rodriguez, Benjamin
Xia, Zheng
Hannah, Rebecca
Wang, Hui
Le, Thuc
Faull, Kym F.
Chen, Rui
Gu, Hongcang
Bock, Christoph
Meissner, Alexander
Göttgens, Berthold
Darlington, Gretchen J.
Li, Wei
Goodell, Margaret A.

May 2014

SummaryTo investigate the cell-intrinsic aging mechanisms that erode the function of somatic stem ce...

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 3: Table S3. of Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling

Anthony Zannas (3577409)
Janine Arloth (434022)
Tania Carrillo-Roa (3577415)
Stella Iurato (3448718)
Simone Röh (434023)
Kerry Ressler (3503072)
Charles Nemeroff (3577418)
Alicia Smith (3448658)
Bekh Bradley (3577412)
Christine Heim (722556)
Andreas Menke (418090)
Jennifer Lange (3577421)
Tanja Brückl (418088)
Marcus Ising (195804)
Naomi Wray (3449882)
Angelika Erhardt (263710)
Elisabeth Binder (3448661)
Divya Mehta (138812)

December 2015

WebGestalt Disease enrichment analysis of the set of unique DEX-regulated genes (n = 139) with TSS n...

Additional file 3: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Abstract

Extracted data

Additional file 3: of LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

Abstract

Extracted data

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