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GenomicsChIP-Seq of Myf5, MyoD, Snai1, HDAC1, HDAC2, E47 and empty vector controls in mouse skeletal myoblasts or myotubes
In skeletal myogenesis, the transcription factor MyoD activates distinct transcriptional programs in progenitors compared to terminally differentiated cells. Using ChIP-seq and gene expression analyses, we show that in primary myoblasts, Snail-HDAC1/2 repressive complex bind and exclude MyoD from it...
ORGANISM(S): Mus musculus 
2012-07-04 | E-GEOD-24852 | biostudies-arrayexpress
GenomicsDissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [ChIP-seq]
Retinoic acid (RA) triggers physiological processes by activating heterodimeric transcription factors comprising retinoic acid (RARa,b,g) and retinoid X (RXRa,b,g) receptors. How a single signal induces highly complex temporally controlled networks that ultimately orchestrate physiological processes...
ORGANISM(S): Mus musculus 
2011-10-11 | E-GEOD-30538 | biostudies-arrayexpress
TranscriptomicsAn RNA-Seq Transcriptome Analysis of Pi Deficient White Lupin Reveals Novel Insights Into Phosphorus Acclimation in Plants
Phosphorus, in its orthophosphate form (Pi), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole genome molecular mechanisms contributing to plant acclimation to Pi deficiency remain largely unknown. White lupin (Lupinus albus L.) has evolved uniq...
ORGANISM(S): Lupinus albus 
2012-11-29 | E-GEOD-31132 | biostudies-arrayexpress
TranscriptomicsUsing RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems
Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. The application of genomic approaches would advance development of alfalfa as a cellulosic feedstock. However, the genomics of alfalfa, a non-model species, is sti...
ORGANISM(S): Medicago sativa 
2011-04-21 | E-GEOD-26757 | biostudies-arrayexpress
GenomicsMapping Novel Chromatin Regions Using Sono-Seq
We found that sonication of crosslinked chromatin produces breaks at non-random sites in DNA and can be used to map sites of high chromatin accessibility when combined with high-throughput tag sequencing using the GA II platform from Illumina. This technique, which we named Sono-Seq, can be a simple...
ORGANISM(S): Homo sapiens 
2008-12-18 | E-GEOD-14022 | biostudies-arrayexpress
GenomicsGenome-wide profile of the SWI/SNF chromatin remodeling complex
A systems understanding of nuclear organization and events is critical for determining how cells divide, differentiate and respond to stimuli and for identifying the causes of diseases. Chromatin remodeling complexes such as SWI/SNF have been implicated in a wide variety of cellular processes includ...
ORGANISM(S): Homo sapiens 
2011-01-10 | E-GEOD-24397 | biostudies-arrayexpress
GenomicsSnail regulates MyoD binding-site occupancy to direct enhancer switching and differentiation-specific transcription in myogenesis
This SuperSeries is composed of the following subset Series: GSE24811: Time Series of Mouse skeletal muscle cell differentiation GSE24852: ChIP-Seq of MyoD, Myf5, Snai1, HDAC1, HDAC2, E47 and empty vector controls in mouse skeletal myoblasts or myotubes GSE38236: RNA-Seq of si-Snai1, si-Snai2, si-Sn...
ORGANISM(S): Mus musculus 
2012-07-04 | E-GEOD-24904 | biostudies-arrayexpress
GenomicsSingle-tube Linear DNA amplification (LinDA) for robust ChIP-seq
Genome-wide profiling of transcription factors based on massive parallel sequencing of immunoprecipitated chromatin (ChIP-seq) requires nanogram amounts of DNA. Here we describe a high-fidelity, single-tube linear DNA amplification method (LinDA) for ChIP-seq and reChIP-seq with picogram DNA amounts...
ORGANISM(S): Homo sapiens 
2011-10-11 | E-GEOD-32332 | biostudies-arrayexpress
GenomicsSMN and Symmetric Arginine Dimethylation of RNAP II CTD Control Termination
The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) subunit POLR2A is a platform for modifications specifying the recruitment of factors that regulate transcription, mRNA processing, and chromatin remodeling. Here, we show that a CTD arginine residue (R1810 in human) that is conserved acr...
ORGANISM(S): Homo sapiens 
2015-12-31 | E-GEOD-73379 | biostudies-arrayexpress
UnknownMultiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas.
Not available
S-EPMC6934292 | biostudies-literature
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