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GenomicsH3K27Ac and CENPA ChIP-seq experiments for human TeloHAEC cells
This data contributes to a telomere-to-telomere genome assembly and annotation of the naked mole-rat, Heterocephalus glaber. To epigenetically annotate centromeres, we performed CENPA ChIP-seq experiments in the male subordinate NMR livers. To ensure antibody quality, as this was the first time CENP...
ORGANISM(S): Homo sapiens 
2026-08-05 | E-MTAB-17311 | biostudies-arrayexpress
GenomicsH3K27Ac and CENPA ChIP-seq experiments for the naked mole-rat liver
This data contributes to a telomere-to-telomere genome assembly and annotation of the naked mole-rat, Heterocephalus glaber. To epigenetically annotate centromeres, we performed CENPA ChIP-seq experiments in the male subordinate NMR livers. These experiments included an Input control, and a H3K27Ac ...
ORGANISM(S): Heterocephalus glaber 
2026-08-05 | E-MTAB-17296 | biostudies-arrayexpress
GenomicsDUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes
Ectopic expression of the double homeodomain transcription factor DUX4 causes facioscapulohumeral muscular dystrophy (FSHD). Mechanisms of action of DUX4 are currently unknown. Using immortalized human myoblasts with a titratable DUX4 transgene, we identify by mass spectrometry an interaction betwee...
ORGANISM(S): Homo sapiens 
2016-03-10 | E-GEOD-78158 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse brain from animals treated with cocaine vs controls
Several recent reports show that the cerebral cortex in humans and animals with altered expressions of Wnt/cadherin network-associate molecules display cytoarchitectural abnormalities reminiscent of cortical dysplasias seen in some (mouse-, rat-, and monkey-based) animal models of prenatal cocaine e...
ORGANISM(S): Mus musculus 
2008-06-15 | E-GEOD-6628 | biostudies-arrayexpress
GenomicsHydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster
This SuperSeries is composed of the following subset Series: GSE32362: Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster (Illumina HumanMethylation450 BeadChip) GSE33129: Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mamm...
ORGANISM(S): Homo sapiens 
2012-05-02 | E-GEOD-33130 | biostudies-arrayexpress
GenomicsHydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster (MeDIP-Seq)
Differentiation is accompanied by extensive epigenomic reprogramming, leading to the repression of stemness factors and the transcriptional maintenance of activated lineage-specific genes. Here we used the mammalian Hoxa cluster of developmental genes as a model system to follow changes in DNA modif...
ORGANISM(S): Homo sapiens 
2012-05-02 | E-GEOD-33129 | biostudies-arrayexpress
TranscriptomicsRB is a cell cycle-regulated repressor of cohesin-dependent loop formation
Chromatin organization and cell cycle are tightly intertwined in eukaryotes, but the underlying mechanisms remain unclear. We investigated how the retinoblastoma protein (RB), a key cell cycle regulator, influences chromatin architecture. Chromosome conformation capture assays reveal that RB loss in...
ORGANISM(S): Homo sapiens 
2024-11-01 | E-MTAB-13566 | biostudies-arrayexpress
TranscriptomicsTranscriptional profiling of dentate granule cells in 4 rat epilepsy models
Global expression profiling of epileptogenesis has been confounded by variability across laboratories, epilepsy models, tissue sampled and experimental platforms, with the result that very few genes demonstrate consistent expression changes. The present study minimizes these confounds by combining ...
ORGANISM(S): Rattus norvegicus 
2013-06-08 | E-GEOD-47752 | biostudies-arrayexpress
GenomicsSemiconductor-based sequencing of genome-wide DNA methylation states
Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used approach to study DNA methylation genome-wide. Here, we present a novel MeDIP-Seq protocol compatible with the Ion Torrent semiconductor-based sequencing platform that is scalable and accurately identifies sites of differe...
ORGANISM(S): Homo sapiens 
2015-06-10 | E-GEOD-61968 | biostudies-arrayexpress
GenomicsChIP-Seq of H3K9 acetylation for wildtype and ada2Δ cells in Cryptococcus neoformans
SAGA member Ada2 is required for the majority of H3K9 acetylation in C. neoformans. To identify specific genomic loci that exhibit Ada2-dependent H3K9 acetylation, we performed ChIP-Seq against H3K9ac in wildtype and ada2Δ cells. ChIP-Seq was performed using antibodies for H3K9ac in KN99 wildtype ce...
ORGANISM(S): Cryptococcus neoformans 
2012-01-01 | E-GEOD-32075 | biostudies-arrayexpress
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