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GenomicsGenome-wide maps of chromatin state in pluripotent and lineage-committed cells
Genome-wide maps of chromatin state (H3K4me3, H3K9me3, H3K27me3, H3K36me3, H4K20me3) in pluripotent and lineage-committed cells We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four b...
ORGANISM(S): Mus musculus 
2008-07-24 | E-GEOD-12241 | biostudies-arrayexpress
GenomicsEpigenomic profiling of 3T3-L1 adipogenesis
3T3-L1 pre-adipocyte cells were grown to confluence and induced to differentiate in adipogenic media. Examination of 6 histone modifications and CTCF at 4 time points and PPARG at 1 time point using ChIP-Seq
ORGANISM(S): Mus musculus 
2010-09-30 | E-GEOD-21365 | biostudies-arrayexpress
GenomicsEpigenomic profiling of hASC adipogenesis
hASC pre-adipocyte cells were grown to confluence and induced to differentiate in adipogenic media. Examination of 6 histone modifications and CTCF at 4 time points and PPARG at 1 time point using ChIP-Seq
ORGANISM(S): Homo sapiens 
2010-09-30 | E-GEOD-21366 | biostudies-arrayexpress
GenomicsCharacterizing the profiles of Ebf1 in mouse fat cells (ChIP-seq)
ChIP-seq data from mouse adipocyte. Mature 3T3-L1 adipocytes were cross-linked with 1% formaldehyde 10 days after induction with MDI. Frozen cell pellets were submitted to the Broad Institute for subsequent analysis of Ebf1-bound regions using anti-Ebf1 antibody (Abnova H00001879-M01).
ORGANISM(S): Mus musculus 
2014-06-10 | E-GEOD-58330 | biostudies-arrayexpress
TranscriptomicsSystematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
We apply a massively parallel reporter assay (MPRA) that relies on mRNA and plasmid tag sequencing (Tag-Seq) to compare the regulatory activities of more than 27,000 distinct variants of two inducible enhancers in human cells: a synthetic cAMP-regulated enhancer and the virus-inducible interferon be...
ORGANISM(S): Escherichia coli 
2012-02-26 | E-GEOD-31982 | 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
GenomicsA unique regulatory phase of DNA methylation in the early mammalian embryo
DNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of global cytosine methylation at fertilization, followed by passive depletion that reaches a minimum at the blastocyst stage. However, this model is based on limit...
ORGANISM(S): Mus musculus 
2012-03-28 | E-GEOD-34864 | 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
TranscriptomicsSystematic dissection of regulatory motifs in 2,000 predicted human enhancers using a massively parallel reporter assay
We employ a massively parallel reporter assay (MPRA) to measure the ex vivo activities of hundreds of K562 and HepG2 enhancers with known transcription factor motif instances. For seven selected motifs that correspond to known or predicted activators and repressors in the two cell types, we make dir...
ORGANISM(S): Escherichia coli 
2013-03-15 | E-GEOD-33367 | biostudies-arrayexpress
GenomicsGenome-wide maps of chromatin state in C2C12 myoblast cells and myotubes.
We did ChIP-seq with anti- H3K4me3, H3K4me1, H3K4me2, H3K27me3, H3K27ac, and H3K36me3 antibodies in both C2C12 myoblasts and myotubes Examination of 6 different histone modifications in 2 cell types.
ORGANISM(S): Mus musculus 
2013-08-24 | E-GEOD-33227 | biostudies-arrayexpress
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