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TranscriptomicsCHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data
Capture Hi-C (CHi-C) is a state-of-the art method for profiling chromosomal interactions involving targeted regions of interest (such as gene promoters) globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other ...
ORGANISM(S): Mus musculus 
2016-05-18 | E-GEOD-81503 | biostudies-arrayexpress
ProteomicsPanorama of ancient metazoan macromolecular complexes: Dictyostelium discoideum
By combining extensive biochemical fractionation with quantitative mass spectrometry, we directly examined the composition of soluble multiprotein complexes among diverse animal models. The project has been jointly supervised by Andrew Emili and Edward M. Marcotte. Project website: http://metazoa.m...
ORGANISM(S): Dictyostelium discoideum AX4 Dictyostelium discoideum (Slime mold) 
2015-06-17 | PXD002320 | Pride
Lc-msms Conservation Metazoan Biofractionation Across species 
GenomicsPromoter capture mESC and fetal liver
Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in HiC libraries from mouse ESC and E14.5 fetal liver. Pl...
ORGANISM(S): Mus musculus 
2015-02-01 | E-MTAB-2414 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse Apoe knockouts treated with SRM2975 and C57Bl/6 mice treated with exhaust particles reveals Serum amyloid and serum amyloid P are not induced in response to diesel exhaust particles or carbon black
W evaluated an experimental particle exposure model, including markers of the acute phase system assessed as the hepatic mRNA expression of Sap, the murine homologue of CRP, and Saa1 and Saa3. Experiment Overall Design: 12-13 weeks old Apoe knockout mice (C57BL/6-Apoe tm1) mice were injected intrape...
ORGANISM(S): Mus musculus 
2009-05-02 | E-GEOD-11346 | biostudies-arrayexpress
UnknownA comparison of balloon- versus stent-based approach for dominant strictures in primary sclerosing cholangitis: a meta-analysis.
Not available
S-EPMC9062839 | biostudies-literature
GenomicsGenome-wide binding of STAT3 in peritoneal macrophages
To try to identify the mechanism of STAT3’s indirect action we have used a genomic approach to map the binding sites of STAT3 within the genome and also used RNA-seq technology to map the changes in RNA expression and transcript isoforms in response to IL-10. Examination of STAT3 binding by ChIP-s...
ORGANISM(S): Mus musculus 
2012-02-13 | E-GEOD-31529 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse lung tissue after exposure to mainstream tobacco smoke
We have examined the impact of subchronic levels of tobacoo smoke on murine lungs. We have used high density DNA microarray and analysed lung tissues from mice exposed to mainstream tobacco smoke (MTS). Our results reveal induction of inflammatory cytokine interleukin-6 (IL-6) and its antagonist sup...
ORGANISM(S): Mus musculus 
2009-09-18 | E-GEOD-12930 | biostudies-arrayexpress
GenomicsChIP-seq of HNF4A and GATA6 in oesophageal adenocaricnoma OE19 cells
The genome-wide binding sites of transcription factors provide insight into their regulatory function. We used chromatin immunoprecipitaition with high-throughput sequencing (ChIP-seq) to identify the genomic binding sites of HNF4A and GATA6 in OE19 cells.
ORGANISM(S): Homo sapiens 
2019-02-09 | E-MTAB-6858 | biostudies-arrayexpress
GenomicsH2A.X native ChIP-Seq in TSC; Histone Variant H2A.X Mediated Epigenetic Mechanisms are Critical for Pluripotency in ES and iPS Cells
With the advent of the induced pluripotent stem cell (iPSC) technology, how to distinguish the developmental potentials of the iPSC clones with molecular approaches becomes an imperative issue. Herein, we demonstrated that histone variant H2A.X plays an unexpected role in distinguishing the develop...
ORGANISM(S): Mus musculus 
2014-09-07 | E-GEOD-57216 | 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
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