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GenomicsGenome-wide chromatin state maps of ES cells, ES-derived neural progenitor cells and brain tissue
Genome-wide chromatin state maps of murine embryonic stem (ES) cells, ES-derived neural progenitor cells and whole brain tissue. The data were generated to examine the correlation between histone and DNA methylation during lineage-commitment. Keywords: High-throughput ChIP-sequencing, Illumina, cell...
ORGANISM(S): Mus musculus 
2008-07-05 | E-GEOD-11172 | biostudies-arrayexpress
TranscriptomicslincRNAs act in the circuitry controlling pluripotency and differentiation
While thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in mammals, few have been functionally characterized leading to debate about their biological role. To address this, we performed loss-of-function studies on most lincRNAs expressed in mouse embryonic stem cells (ESC...
ORGANISM(S): Mus musculus 
2011-08-29 | E-GEOD-30245 | biostudies-arrayexpress
GenomicsMapping polycomb complexes in human and mouse embryonic stem cells
In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2000 genes. To gain insight into the structure and function of bivalent domains, we m...
ORGANISM(S): Mus musculus 
2008-11-01 | E-GEOD-13084 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse ES cells, neural precursor cells and embryonic fibroblasts
Expression profiles for isogenic (129SvJae x C57BL/6) murine embryonic stem (ES) cells, neural precursors (NPC) obtained through in vitro differentiation of the ES cells, and embryonic fibroblasts (MEF) obtained at day 13.5. Experiment Overall Design: 3 replicates of wt ES cells, 3 replicates of wt...
ORGANISM(S): Mus musculus 
2008-06-15 | E-GEOD-8024 | biostudies-arrayexpress
GenomicsGenome-scale DNA methylation maps of pluripotent and differentiated cells
We report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput Reduced Representation Bisulfite Sequencing (RRBS) and single-molecule-based sequencing, we generated DNA methylation maps covering the vast majority of C...
ORGANISM(S): Mus musculus 
2008-07-06 | E-GEOD-11034 | biostudies-arrayexpress
GenomicsXist exploits three-dimensional chromosome architecture to spread across the X-chromosome
Many large noncoding RNAs (lncRNAs) regulate chromatin, but the mechanisms by which they localize to genomic targets remain unexplored. Here we investigate the localization mechanisms of Xist during X-chromosome inactivation (XCI), a paradigm of lncRNA-mediated chromatin regulation. During the maint...
ORGANISM(S): Mus musculus 
2013-05-30 | E-GEOD-46918 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse embryonic stem cell-derived astrocytes
Expression profiles for Gfap-positive astrocytes obtained by in vitro differentiation of 129SvJae x C57BL/6 murine embryonic stem (ES) cells. Generated to examine the relationship between expression levels and DNA methylation patterns. Experiment Overall Design: 3 replicates of ES-derived astrocyte...
ORGANISM(S): Mus musculus 
2008-10-20 | E-GEOD-11483 | biostudies-arrayexpress
TranscriptomicsMany Human Large Intergenic Non-coding RNAs Associate with Chromatin Modifying Complexes and Affect Gene Expression
We recently showed that the mammalian genome encodes more than a thousand large intergenic non-coding RNAs (lincRNAs) that are clearly conserved across mammals and thus functional. Gene expression patterns have implicated these lincRNAs in diverse biological processes including cell cycle regulatio...
ORGANISM(S): Homo sapiens 
2009-07-09 | E-GEOD-16226 | biostudies-arrayexpress
TranscriptomicsExpression profiling of 3T3-L1 adipogenesis
3T3-L1 pre-adipocyte cells were grown to confluence and induced to differentiate in adipogeneic media. Two technical replicates from four time points relative to induction of adipogenesis (day 0)
ORGANISM(S): Mus musculus 
2010-09-30 | E-GEOD-20696 | biostudies-arrayexpress
TranscriptomicsExpression profiling of human adipose stromal cell (hASC) adipogenesis
Human abdominal adipose tissue was obtained with informed consent from a 33-year old Caucasian female (BMI = 32.96 Kg/m2) undergoing lipoaspiration. Adipose stromal cells (hASCs) were isolated and differentiated into adipocytes in vitro. Two technical replicates from 9 time points realtive to induct...
ORGANISM(S): Homo sapiens 
2010-09-30 | E-GEOD-20697 | biostudies-arrayexpress
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