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GenomicsGenome wide mapping of Jarid2 and Suz12 binding sites in mouse ES cells before and after Jarid2 depletion
We analyzed the overlap in genome wide binding sites between Jarid2 and Suz12 in mouse ES cells and find that Jarid2 and Suz12 peaks have an high degree (90%) of overlap. Moreover we analyzed the effect of Jarid2 down regulation on genome wide Suz12 binding sites and found that Loss of Jarid2 lead t...
ORGANISM(S): Mus musculus 
2010-01-27 | E-GEOD-19365 | biostudies-arrayexpress
GenomicsSequence and expression analysis of human chromosome 20 gaps
The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 currently has three remaining un-sequenced gaps on its q-arm. All three gaps are within gene-dense regions, or overlap loci ...
ORGANISM(S): Homo sapiens 
2012-04-17 | E-GEOD-35405 | biostudies-arrayexpress
GenomicsGenome-wide mapping of H3K4me3 and of PHF8 and ZNF711 binding sites in SH-SY5Y cells
We analyzed the genome wide binding sites for the potential XLMR genes PHF8 and ZNF711 in the neuroblastoma cell line SH-SY5Y using antibodies specific for PHF8 and ZNF711 and correlated this with binding pattern of H3K4me3. The total number of peaks detected for PHF8 based on 9.8 million sequence...
ORGANISM(S): Homo sapiens 
2010-03-08 | E-GEOD-20673 | biostudies-arrayexpress
GenomicsREST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells
Genome-wide analysis of REST and Polycomb binding in Rest-/- and Eed-/- mouse embryonic stem (mES) cells showed that Rest was required for PRC1 recruitment to a subset of Polycomb regulated neuronal genes. Furthermore, we found that PRC1 can be recruited to Rest binding sites independently of CpG is...
ORGANISM(S): Mus musculus 
2013-06-20 | E-GEOD-48122 | biostudies-arrayexpress
TranscriptomicsLong non-coding RNA HOTAIR is an independent prognostic marker of metastasis in estrogen receptor positive primary breast cancer
Expression of HOX transcript antisense intergenic RNA (HOTAIR)—a long intergenic non-coding RNA (lincRNA)—has been examined in a variety of human cancers, and overexpression of HOTAIR is correlated with poor survival among breast, colon, and liver cancer patients. In this retrospective study, we exa...
ORGANISM(S): Homo sapiens 
2013-11-29 | E-GEOD-48408 | biostudies-arrayexpress
TranscriptomicsTGF-b Signaling Is Associated with Endocytosis at the Pocket Region of the Primary Cilium
Digital gene expression tag profiling of P19CL6 cell model during differentiation to cardiomyocytes Four replicates were anlyzed at five time-points during differentiation; day 1, day 4, day 7, day 10 and day 14. Spontanously beating cardiomyocytes was observed at day 14 Spreadsheet with Log2 differ...
ORGANISM(S): Mus musculus 
2013-06-06 | E-GEOD-47656 | biostudies-arrayexpress
TranscriptomicsClassifications within Molecular Subtypes Enables Identification of BRCA1/BRCA2 Mutation Carriers by RNA Tumor Profiling
Pathogenic germline mutations in BRCA1 or BRCA2 are detected in less than one third of families with a strong history of breast cancer. It is therefore expected that mutations still remain undetected by currently used screening methods. In addition, a growing number of BRCA1/2 sequence variants of u...
ORGANISM(S): Homo sapiens 
2013-06-28 | E-GEOD-40115 | biostudies-arrayexpress
GenomicsIdentification of the BRD1 interactome and its impact on schizophrenia risk
We identified protein-protein interactions and chromatin binding sites for two isforms of BRD1 (BRD1-S and BRD1-L) using Co-IP MS/MS and ChIP-seq. BRD1 isoforms were cloned, epitope-tagged (pcDNA 6 V5-His6, Lifetechnologies) and stably expressed in HEK293T cells. Chromatin immunoprecipitations were ...
ORGANISM(S): Homo sapiens 
2015-10-29 | E-GEOD-62811 | biostudies-arrayexpress
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