Stem Cell Commons

The Stem Cell Commons is a repository of data belonging to members of the Harvard Stem Cell Institute (HSCI).

Featured Dataverses

In order to use this feature you must have at least one published dataverse.

Publish Dataverse

Are you sure you want to publish your dataverse? Once you do so it must remain published.

Publish Dataverse

This dataverse cannot be published because the dataverse it is in has not been published.

Delete Dataverse

Are you sure you want to delete your dataverse? You cannot undelete this dataverse.

1 to 8 of 8 Results

Comparative profiling of chromatin state maps and transcription factor occupancy during human fetal and adult erythropoiesis [Histone Modification] Oct 30, 2020 - Orkin Lab Xu, Jian; Zhen, Shao; Glass, Kimberly; Bauer, Daniel E.; Pinello, Luca; Van Handel, Ben; Hou, Serena; Stamatoyannopoulos, John A.; Mikkola, Hanna K.A.; Yuan, Guo-Cheng; Orkin, Stuart H., 2020, "Comparative profiling of chromatin state maps and transcription factor occupancy during human fetal and adult erythropoiesis [Histone Modification]", https://doi.org/10.7910/DVN/Z6OX6R, Harvard Dataverse, V1 Gene-distal enhancers are critical for tissue-specific gene expression, but their genomic determinants within a specific lineage at different stages of development are unknown. Here we profile chromatin state maps, transcription factor occupancy, and gene expression profiles duri...
Comparative profiling of chromatin state maps and transcription factor occupancy during human fetal and adult erythropoiesis [Transcription Factor Binding] Oct 30, 2020 - Orkin Lab Xu, Jian; Zhen, Shao; Glass, Kimberly; Bauer, Daniel E.; Pinello, Luca; Van Handel, Ben; Hou, Serena; Stamatoyannopoulos, John A.; Mikkola, Hanna K.A.; Yuan, Guo-Cheng; Orkin, Stuart H., 2020, "Comparative profiling of chromatin state maps and transcription factor occupancy during human fetal and adult erythropoiesis [Transcription Factor Binding]", https://doi.org/10.7910/DVN/P75S6Z, Harvard Dataverse, V1 Gene-distal enhancers are critical for tissue-specific gene expression, but their genomic determinants within a specific lineage at different stages of development are unknown. Here we profile chromatin state maps, transcription factor occupancy, and gene expression profiles duri...
Identification of genes regulated by Rcor1 in CD71+, TER119- erythroid progenitors using mRNA-seq analysis Oct 30, 2020 - Orkin Lab Yao, Huilan; Goldman, Devorah C.; Nechiporuk, Tamilla; Kawane, Sunita; McWeeney, Shannon K.; Tyner, Jeffrey W.; Fan, Guang; Kerenyi, Marc A.; Orkin, Stuart H.; Fleming, William H.; Mandel, Gail, 2020, "Identification of genes regulated by Rcor1 in CD71+, TER119- erythroid progenitors using mRNA-seq analysis", https://doi.org/10.7910/DVN/RGPBWN, Harvard Dataverse, V1 Transcription cofactor Rcor1 has been linked biochemically both to neurogenesis and hematopoiesis. Here we studied the function of Rcor1 in vivo and showed it is essential to erythropoeisis during embryonic development. Rcor1 mutant proerythroblasts, unlike normal cells, can form...
Histone Demethylase Lsd1 is Required to Repress Hematopoietic Stem and Progenitor Cell Signatures During Blood Cell Maturation Oct 30, 2020 - Orkin Lab Kerenyi, Marc A.; Zhen, Shao; Hsu, Yu-Jung; Guoji, Guo; Sidinh, Luc; O’Brien, Kassandra; Fujiwara, Yuko; Peng, Cong; Nguyen, Minh; Orkin, Stuart H., 2020, "Histone Demethylase Lsd1 is Required to Repress Hematopoietic Stem and Progenitor Cell Signatures During Blood Cell Maturation", https://doi.org/10.7910/DVN/AVCOF5, Harvard Dataverse, V1 Here, we describe that lysine-specific demethylase 1 (Lsd1/KDM1a), which demethylates histone H3 on Lys4 or Lys9 (H3K4/K9), is an indispensible epigenetic governor of hematopoietic differentiation. Integrative genomic analysis, combining global occupancy of Lsd1, genome-wide anal...
ChIP-seq analysis of chromatin state plasticity in primary human adult erythroid progenitor cells Oct 30, 2020 - Orkin Lab Pinello, Luca; Xu, Jian; Orkin, Stuart H.; Yuan, Guo-Cheng, 2020, "ChIP-seq analysis of chromatin state plasticity in primary human adult erythroid progenitor cells", https://doi.org/10.7910/DVN/FFPCJX, Harvard Dataverse, V1 We report a computational approach for investigation of chromatin state plasticity. We applied this approach to investigate an ENCODE ChIP-seq dataset profiling the genome-wide distribution of H3K27me3 in 19 human cell lines. We found that high plasticity regions (HPRs) can be di...
Orkin Lab(Harvard University) Oct 30, 2020
A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis Oct 30, 2020 - Zon Lab Paik, Elizabeth J.; Mahony, Shaun; White, Richard M.; Price, Emily N.; DiBiase, Anthony; Dorjsuren, Bilguujin; Mosimann, Christian; Davidson, Alan J.; Gifford, David; Zon, Leonard I., 2020, "A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis", https://doi.org/10.7910/DVN/0XYJJW, Harvard Dataverse, V1 Deletion of caudal/cdx genes alters hox gene expression and causes defects in posterior tissues and hematopoiesis. Yet, the defects in hox gene expression only partially explain these phenotypes. To gain deeper insight into Cdx4 function, we performed ChIP-seq combined with gene...
Zon Lab(Harvard University) Oct 30, 2020

Comparative profiling of chromatin state maps and transcription factor occupancy during human fetal and adult erythropoiesis [Histone Modification]

Oct 30, 2020 - Orkin Lab

Xu, Jian; Zhen, Shao; Glass, Kimberly; Bauer, Daniel E.; Pinello, Luca; Van Handel, Ben; Hou, Serena; Stamatoyannopoulos, John A.; Mikkola, Hanna K.A.; Yuan, Guo-Cheng; Orkin, Stuart H., 2020, "Comparative profiling of chromatin state maps and transcription factor occupancy during human fetal and adult erythropoiesis [Histone Modification]", https://doi.org/10.7910/DVN/Z6OX6R, Harvard Dataverse, V1

Gene-distal enhancers are critical for tissue-specific gene expression, but their genomic determinants within a specific lineage at different stages of development are unknown. Here we profile chromatin state maps, transcription factor occupancy, and gene expression profiles duri...

Comparative profiling of chromatin state maps and transcription factor occupancy during human fetal and adult erythropoiesis [Transcription Factor Binding]

Oct 30, 2020 - Orkin Lab

Xu, Jian; Zhen, Shao; Glass, Kimberly; Bauer, Daniel E.; Pinello, Luca; Van Handel, Ben; Hou, Serena; Stamatoyannopoulos, John A.; Mikkola, Hanna K.A.; Yuan, Guo-Cheng; Orkin, Stuart H., 2020, "Comparative profiling of chromatin state maps and transcription factor occupancy during human fetal and adult erythropoiesis [Transcription Factor Binding]", https://doi.org/10.7910/DVN/P75S6Z, Harvard Dataverse, V1

Identification of genes regulated by Rcor1 in CD71+, TER119- erythroid progenitors using mRNA-seq analysis

Oct 30, 2020 - Orkin Lab

Yao, Huilan; Goldman, Devorah C.; Nechiporuk, Tamilla; Kawane, Sunita; McWeeney, Shannon K.; Tyner, Jeffrey W.; Fan, Guang; Kerenyi, Marc A.; Orkin, Stuart H.; Fleming, William H.; Mandel, Gail, 2020, "Identification of genes regulated by Rcor1 in CD71+, TER119- erythroid progenitors using mRNA-seq analysis", https://doi.org/10.7910/DVN/RGPBWN, Harvard Dataverse, V1

Transcription cofactor Rcor1 has been linked biochemically both to neurogenesis and hematopoiesis. Here we studied the function of Rcor1 in vivo and showed it is essential to erythropoeisis during embryonic development. Rcor1 mutant proerythroblasts, unlike normal cells, can form...

Histone Demethylase Lsd1 is Required to Repress Hematopoietic Stem and Progenitor Cell Signatures During Blood Cell Maturation

Oct 30, 2020 - Orkin Lab

Kerenyi, Marc A.; Zhen, Shao; Hsu, Yu-Jung; Guoji, Guo; Sidinh, Luc; O’Brien, Kassandra; Fujiwara, Yuko; Peng, Cong; Nguyen, Minh; Orkin, Stuart H., 2020, "Histone Demethylase Lsd1 is Required to Repress Hematopoietic Stem and Progenitor Cell Signatures During Blood Cell Maturation", https://doi.org/10.7910/DVN/AVCOF5, Harvard Dataverse, V1

Here, we describe that lysine-specific demethylase 1 (Lsd1/KDM1a), which demethylates histone H3 on Lys4 or Lys9 (H3K4/K9), is an indispensible epigenetic governor of hematopoietic differentiation. Integrative genomic analysis, combining global occupancy of Lsd1, genome-wide anal...

ChIP-seq analysis of chromatin state plasticity in primary human adult erythroid progenitor cells

Oct 30, 2020 - Orkin Lab

Pinello, Luca; Xu, Jian; Orkin, Stuart H.; Yuan, Guo-Cheng, 2020, "ChIP-seq analysis of chromatin state plasticity in primary human adult erythroid progenitor cells", https://doi.org/10.7910/DVN/FFPCJX, Harvard Dataverse, V1

We report a computational approach for investigation of chromatin state plasticity. We applied this approach to investigate an ENCODE ChIP-seq dataset profiling the genome-wide distribution of H3K27me3 in 19 human cell lines. We found that high plasticity regions (HPRs) can be di...

Orkin Lab(Harvard University)

Oct 30, 2020

A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis

Oct 30, 2020 - Zon Lab

Paik, Elizabeth J.; Mahony, Shaun; White, Richard M.; Price, Emily N.; DiBiase, Anthony; Dorjsuren, Bilguujin; Mosimann, Christian; Davidson, Alan J.; Gifford, David; Zon, Leonard I., 2020, "A Cdx4-Sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis", https://doi.org/10.7910/DVN/0XYJJW, Harvard Dataverse, V1

Deletion of caudal/cdx genes alters hox gene expression and causes defects in posterior tissues and hematopoiesis. Yet, the defects in hox gene expression only partially explain these phenotypes. To gain deeper insight into Cdx4 function, we performed ChIP-seq combined with gene...

Zon Lab(Harvard University)

Oct 30, 2020

Add Data

Share Dataverse

Link Dataverse

Reset Modifications