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GenomicsChromatin architecture organized by histone variants H3.3 and H2A.Z in the human genome
To understand how chromatin structure is organized by different histone variants, we have measured the genome-wide distribution of nucleosome core particles (NCPs) containing the histone variants H3.3 and H2A.Z in human cells. We find that a special class of NCPs containing both variants is enriched...
ORGANISM(S): Homo sapiens 
2009-07-26 | E-GEOD-13308 | biostudies-arrayexpress
TranscriptomicsRegulation of pluripotency and self-renewal of ES cells through epigenetic-threshold modulation and mRNA pruning
The core pluripotency factors (Oct4, Sox2, and Nanog), the Myc network, and the chromatin-modifying complexes such as PRC2 ensure the pluripotency and self-renewal of ES cells (ESC). How these factors coordinate with one another remains poorly understood. We report that Utf1, a target of Oct4 and So...
ORGANISM(S): Mus musculus 
2012-10-26 | E-GEOD-39513 | biostudies-arrayexpress
GenomicsDNA double-strand breaks induced by high NaCl occur predominantly in gene deserts
High concentration of NaCl increases DNA breaks both in cell culture and in vivo. The breaks remain elevated as long as NaCl concentration remains high and are rapidly repaired when the concentration is lowered. Repair of the breaks after NaCl is reduced is accompanied by formation of foci containi...
ORGANISM(S): Mus musculus 
2011-11-21 | E-GEOD-32882 | biostudies-arrayexpress
GenomicsesBAF is an essential component of the core pluripotency transcriptional network
Distinctive SWI/SNF-like ATP-dependent chromatin remodeling esBAF complexes are indispensable for the maintenance and pluripotency of mouse embryonic stem (ES) cells. To understand the mechanism underlying the roles of these complexes in ES cells, we performed high-resolution genome-wide mapping of ...
ORGANISM(S): Mus musculus 
2009-01-20 | E-GEOD-14344 | biostudies-arrayexpress
TranscriptomicsDynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq
Both transcription and post-transcriptional processes, such as alternative splicing, play crucial roles in controlling developmental programs in metazoans. Recently emerged RNA-seq method has brought our understanding of eukaryotic transcriptomes to a new level, because it can resolve both gene expr...
ORGANISM(S): Drosophila melanogaster 
2010-05-04 | E-GEOD-16960 | biostudies-arrayexpress
TranscriptomicsGenome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples
DNase I hypersensitive sites (DHSs) provide important information on the presence of transcriptional regulatory elements and the state of chromatin in mammalian cells1, 2, 3. Conventional DNase sequencing (DNase-seq) for genome-wide DHSs profiling is limited by the requirement of millions of cells4,...
ORGANISM(S): Mus musculus 
2015-11-25 | E-GEOD-61844 | biostudies-arrayexpress
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