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TranscriptomicsEpigenetic regulation of Bmp2 and Smad6 in Ras-induced senescence
Epigenetically silenced Ink4a-Arf locus is activated by loss of H3K27me3 in cellular senescence, where secreted factor expression is also involved. Here we analyzed epigenome and transcriptome alteration during Ras-induced senescence using mouse embryonic fibroblast (MEF). Seventeen genes with H3K27...
ORGANISM(S): Mus musculus 
2011-12-22 | E-GEOD-18125 | biostudies-arrayexpress
GenomicsR-loops induce repressive chromatin marks over mammalian gene terminators
The formation of R-loops is a natural consequence of the transcription process, caused by invasion of the DNA duplex by nascent transcripts. These structures have been considered rare transcriptional by-products with potential harmful effects on genome integrity, due to the fragility of the displace...
ORGANISM(S): Homo sapiens 
2014-09-29 | E-GEOD-59878 | biostudies-arrayexpress
TranscriptomicsExpression data of Medicago truncatula Jemalong A17 roots treated with auxin transport inhibitors
Rhizobium and allied bacteria form symbiotic nitrogen-fixing nodules on legume roots. Plant hormones appear to play a role in nodule formation. We treated Medicago truncatula roots with auxin transport inhibitors (ATIs) N-(1-naphthyl)phthalamic acid (NPA) and 2,3,5-triiodobenzoic acid (TIBA) to indu...
ORGANISM(S): Medicago truncatula 
2011-03-26 | E-GEOD-27991 | biostudies-arrayexpress
TranscriptomicsRNA-sequencing analysis of NGN3-GFP positive and negative cells purified from differentiating human embryonic stem cells
NGN3-eGFP could be used to mark endocrine progenitor cells and their progeny in differentiating hESCs, suggesting that profiling analysis of NGN3-eGFP+ cells could lead to the discovery of novel gene participation. Six batches of NGN3-eGFP+ and NGN3-eGFP -cells purified by FACS from a reporter hES c...
ORGANISM(S): Homo sapiens 
2014-09-12 | E-GEOD-54879 | biostudies-arrayexpress
TranscriptomicsEarly effects of cdkf;1 RNAPII CTD Serine-7 kinase mutation on regulation of transcription in 7 days old Arabidopsis seedlings
Serine phosphorylation of conserved Y1S2P3T4S5P6S7 repeats of RNA polymerase II carboxy-terminal domain (RNAPII CTD) plays a central role in the regulation of transcription and co-transcriptional RNA processing. Maintenance of CTD phosphoserine-7 mark in Arabidopsis requires the CDKF;1 kinase, which...
ORGANISM(S): Arabidopsis thaliana 
2011-08-31 | E-GEOD-27687 | biostudies-arrayexpress
TranscriptomicsExpression data of Medicago truncatula skl1-1 roots treated with S. meliloti wild-type or auxin transport inhibitors
Rhizobium and allied bacteria form symbiotic nitrogen-fixing nodules on legume roots. Plant hormones appear to play a role in nodule formation. We treated Medicago truncatula roots with auxin transport inhibitors (ATIs) N-(1-naphthyl)phthalamic acid (NPA) and 2,3,5-triiodobenzoic acid (TIBA) to indu...
ORGANISM(S): Medicago truncatula 
2011-03-25 | E-GEOD-28172 | biostudies-arrayexpress
GenomicsH2A.X native ChIP-Seq in ESC and iPSC: Histone Variant H2A.X Mediated Epigenetic Mechanisms are Critical for Maintaining Genome Stability and Pluripotency in ES and iPS Cells
It is well-known that embryonic stem cells (ESC) are much more sensitive to replication-induced stress than differentiated cells but the underpinning mechanisms are largely unknown. H2A.X, a minor variant of H2A, constitutes only 1-10% of the mammalian genome. H2A.X plays a well-known for role in t...
ORGANISM(S): Mus musculus 
2014-09-07 | E-GEOD-42306 | biostudies-arrayexpress
TranscriptomicsExpression data of Medicago truncatula Jemalong A17 roots treated with S. meliloti exoA mutant or auxin transport inhibitors
Rhizobium and allied bacteria form symbiotic nitrogen-fixing nodules on legume roots. Plant hormones appear to play a role in nodule formation. We treated Medicago truncatula roots with auxin transport inhibitors (ATIs) N-(1-naphthyl)phthalamic acid (NPA) and 2,3,5-triiodobenzoic acid (TIBA) to indu...
ORGANISM(S): Medicago truncatula 
2011-03-25 | E-GEOD-28171 | biostudies-arrayexpress
TranscriptomicsGenes differentially expressed in wild-type Medicago truncatula plants during nodulation
We used an Affymetrix oligonucleotide microarray consisting of 9,935 tentative consensus (TC)sequences, which are based on cDNA libraries (Mitra et al., 2004 [PMID:15220482]). We examined gene expression of wild-type M. truncatula plants after inoculation with wild-type S. meliloti at 1 d, 4 d, 7d,...
ORGANISM(S): Medicago truncatula 
2011-03-26 | E-GEOD-28173 | biostudies-arrayexpress
GenomicsTranscriptional regulation of Tet1 during development
5-hydroxymethylcytosine (5hmC) is a recently discovered epigenetic modification that is lost in human cancers. Formation of 5hmC is catalysed by the Ten eleven translocation (TET) proteins that mediate the sequential oxidation of 5-methylcytosine (5mC) to 5hmC, leading to eventual DNA demethylation....
ORGANISM(S): Mus musculus 
2015-08-04 | E-GEOD-57250 | biostudies-arrayexpress
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