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Genomics5-hydroxymethylcytosine: the sixth DNA base
We performed a meta analysis of publicly available TET1, 5mC, 5hmC and genome wide bisulfite profiling data mostly from mouse embryonic stem cells (ESC). Genome wide chromatin immunoprecipitation combined with deep sequencing (ChIP-seq) has revealed binding of the TET1 protein at CpG-island (CGI) pr...
ORGANISM(S): Mus musculus 
2011-11-24 | E-GEOD-31343 | biostudies-arrayexpress
TranscriptomicsDynamic histone H3 epigenome marking during the intraerythrocytic cycle of P. falciparum
This SuperSeries is composed of the following subset Series: GSE15728: Mapping of H3, H3K4me3, H3K9me3, and H3K9ac on mixed asexual stages of P. falciparum GSE16095: Mapping of H3, H3K4me3 and H3K9ac on Ring and Schizont stages of P. falciparum Refer to individual Series
ORGANISM(S): Plasmodium falciparum 
2010-05-19 | E-GEOD-16096 | biostudies-arrayexpress
GenomicsOncofusion protein AML1-ETO targets ERG factor binding sites in AML
ERG has been identified as an essential factor for the function and maintenance of adult hematopoietic stem cells and high ERG expression is a negative prognostic marker for treatment outcome in AML. The molecular function of ERG and its interplay with other factors is however largely unknown. Here ...
ORGANISM(S): Homo sapiens 
2012-09-18 | E-GEOD-23730 | biostudies-arrayexpress
TranscriptomicsMetagenomic, metatranscriptomic and metaproteomic study of enrichment culture of M. oxyfera (denitrifying methanotroph)
DNA, RNA and protein were extracted from the culture and subjected to massive parallel sequencing and nano-LC-MS-MS respectively Combination of these methods enabled the reconstruction of the complete genome sequence of M oxyfera from the metagenome and identification of the functionally relevant en...
ORGANISM(S): Candidatus Methylomirabilis oxyfera 
2010-03-25 | E-GEOD-18535 | biostudies-arrayexpress
TranscriptomicsRNA-Seq transcriptome profiling of in vitro cultures of migrating porcine primordial germ cells and porcine fetal fibroblasts of mini pig embryos between days 17-24 of gestation
Porcine embryonic germ cells (EGC) are cultured pluripotent cells derived from primordial germ cells (PGC). This study explored the possibilities to establish porcine EGC lines in the domestic breed pig more efficiently and from earlier embryonic stages than reported to date. In vitro culture of PGC...
ORGANISM(S): Sus scrofa 
2011-03-24 | E-GEOD-24220 | biostudies-arrayexpress
TranscriptomicsMetatranscriptomic analysis of an anaerobic ammonium oxidizing community dominated by Kuenenia stuttgartiensis
We compiled a metatranscriptome by extracting total RNA (including ribosomes), reverse transcription and solexa sequencing. We obtained quantitative data on the transcription of each orf to assess the importance of each orf to the metabolism of Kuenenia stuttgartiensis The transcriptomic data are co...
ORGANISM(S): Candidatus Kuenenia stuttgartiensis 
2010-03-25 | E-GEOD-15408 | biostudies-arrayexpress
GenomicsChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands
We used ChIP-Seq to map ERalpha binding sites and to profile changes in RNA polymerase II (RNAPII) occupancy in MCF-7 cells in response to estradiol (E2), tamoxifen or fulvestrant. We identified 10,205 high confidence ERalpha binding sites in response to E2 of which 68% contained an estrogen respons...
ORGANISM(S): Homo sapiens 
2009-03-09 | E-GEOD-14664 | biostudies-arrayexpress
GenomicsGenome-wide profiling of PPAR?:RXR and RNA polymerase II
Genome-wide profiling of PPAR?:RXR and RNA polymerase II reveals temporal activation of distinct metabolic pathways in RXR dimer composition during adipogenesis. Chromatin immunoprecipitation combined with deep sequencing was performed to generate genome-wide maps of peroxisome prolifelator-activat...
ORGANISM(S): Mus musculus 
2008-12-10 | E-GEOD-13511 | biostudies-arrayexpress
TranscriptomicsMapping of H3, H3K4me3, H3K9me3, and H3K9ac on mixed asexual stages of P. falciparum
Epigenome profiling has led to the paradigm that promoters of active genes are decorated with H3K4me3 and H3K9ac marks. Data revealed an extensively euchromatic epigenome with heterochromatin restricted to variant surface antigen gene families (VSA) and a number of genes hitherto unlinked to VSA. Th...
ORGANISM(S): Plasmodium falciparum 
2010-05-19 | E-GEOD-15728 | biostudies-arrayexpress
TranscriptomicsMapping of H3, H3K4me3 and H3K9ac on Ring and Schizont stages of P. falciparum
Epigenome profiling has led to the paradigm that promoters of active genes are decorated with H3K4me3 and H3K9ac marks. These data on synchronized parasites reveals significant developmental stage specificity of the epigenome. In rings, H3K4me3 and H3K9ac are homogenous across the genes marking acti...
ORGANISM(S): Plasmodium falciparum 
2010-05-19 | E-GEOD-16095 | biostudies-arrayexpress
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