Promoter capture Hi-C of CD34+ haematopoietic stem cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Homo sapiens
SUBMITTER: Borbala Mifsud
PROVIDER: E-MTAB-10701 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Chromatin organisation of trophoblast stem cells (TSC) were compared with that of embryonic stem cells (ESC). The method enriches Hi-C libraries, to detect promoter interactions at restriction fragment level. We prepared Hi-C libraries from TSC and ESC (serum grown) samples and enriched them with a promoter capture bait system that captures ~22.000 promoters. Promoter interactions were then analysed using the GOTHiC pipeline.
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Project description: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. Please note additional files included. These files were created using the following protocol: Significantly interacting regions were called using the GOTHiC BioConductor package (http://www.bioconductor.org/packages/devel/bioc/html/GOTHiC.html) as described in (Mifsud et al.).<br>Update on December 2015: the original additional file E-MTAB-2414.additional.1.zip contained an earlier iteration of processed data and not the one that was used for the published paper. The file now contains the correct list of interactions.
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