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GenomicsH3K27me3 ChIP-seq experiment in fruitfly testis somatic gonadal cells
In many metazoans, germ cells are separated from somatic lineages early in development and maintain their identity throughout life. Here we show that a Polycomb group (PcG) component, Enhancer of Zeste [E(z)] H3K27me3-specific methyltransferase, maintains germline identity in Drosophila adult testes...
ORGANISM(S): Drosophila melanogaster 
2014-05-02 | E-GEOD-53238 | biostudies-arrayexpress
GenomicsGenome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3
We developed a system to study the DNA replication-independent turnover nucleosomes containing the histone variant H3.3 in mammalian cells. By measuring the genome-wide incorporation of H3.3 at different time points following epitope-tagged H3.3 expression, we find three categories of H3.3-nucleosom...
ORGANISM(S): Mus musculus 
2013-10-23 | E-GEOD-51505 | biostudies-arrayexpress
TranscriptomicsMapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis
Formation of the blood from self-renewing hematopoietic stem cells to terminal lineages necessarily involves epigenomic modifications of the genome to control regulator and signature gene expression. By analysing the global expression profiles of hematopoietic stem cells (HSCs), in vivo differentiat...
ORGANISM(S): Homo sapiens 
2013-03-25 | E-GEOD-39229 | biostudies-arrayexpress
GenomicsMapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis [ChIP-Seq]
Formation of the blood from self-renewing hematopoietic stem cells to terminal lineages necessarily involves epigenomic modifications of the genome to control regulator and signature gene expression. By analysing the global expression profiles of hematopoietic stem cells (HSCs), in vivo differentiat...
ORGANISM(S): Homo sapiens 
2013-03-25 | E-GEOD-39538 | biostudies-arrayexpress
TranscriptomicsKDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation [RNA-Seq]
Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. Here, we show that KDM5B, which demethylates lysine 4 of histone H3...
ORGANISM(S): Mus musculus 
2014-01-27 | E-GEOD-53090 | biostudies-arrayexpress
TranscriptomicsMapping of INS promoter interactions reveals its role in long-range regulation of SYT8 transcription
Insulin (INS) synthesis and secretion from pancreatic M-NM-2 cells are tightly regulated; their deregulation causes diabetes. Here we map INS-associated loci in human pancreatic islets by 4C and 3C techniques and show that the INS gene physically interacts with the SYT8 gene, located over 300 kb ...
ORGANISM(S): Homo sapiens 
2011-02-22 | E-GEOD-25862 | biostudies-arrayexpress
GenomicsKDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation [ChIP-Seq]
Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. Here, we show that KDM5B, which demethylates lysine 4 of histone H3...
ORGANISM(S): Mus musculus 
2014-01-27 | E-GEOD-53087 | biostudies-arrayexpress
TranscriptomicsMonovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis
We use male gonads isolated from a Drosophila strain that allows us to obtain enough cells at their primitive status as the starting material to study the endogenous chromatin structure of undifferentiated cells using ChIP-seq. We integrate the ChIP-seq data with RNA-seq data that measures the trans...
ORGANISM(S): Drosophila melanogaster 
2010-04-16 | E-GEOD-19325 | biostudies-arrayexpress
TranscriptomicsActive chromatin domains are defined by acetylation islands revealed by genome-wide mapping
The identity and developmental potential of a human cell is specified by its epigenome that is largely defined by patterns of chromatin modifications including histone acetylation. Here we report high-resolution genome-wide mapping of diacetylation of histone H3 at Lys 9 and Lys 14 in resting and ac...
ORGANISM(S): Homo sapiens 
2007-02-05 | E-GEOD-6974 | biostudies-arrayexpress
TranscriptomicsExtended self-renewal and accelerated reprogramming in the absence of Kdm5b [RNA-Seq]
ES cell pluripotency is thought to be regulated in part by H3K4 methylation. However, it is unclear how H3K4 demethylation contributes to ES cell function and participates in iPS cell reprogramming. Here, we show that KDM5B, which demethylates H3K4, is important for ES cell differentiation, and pres...
ORGANISM(S): Mus musculus 
2013-10-14 | E-GEOD-47124 | biostudies-arrayexpress
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