EXPERIMENT_TITLE: GSM2597686: HiC_IMR90_MYOD_DM_Rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For RNASeq: cells were lyzed with Trizol and RNA was extracted following manufacturer's instruction. For Hi-C, DNA crossliked, digested and ligated, ligation products were isolated with streptavidine beads, Hi-C experiment were conducted in biological replicates using DpnIII, according to the protocol published by Rao et al, 2014 with slight modifications RNASeq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit set A RS-122-2101 following Illumina's recomandations. Hi-C experiment were conducted in biological replicates using DpnIII, according to the protocol published by Rao et al, 2014 with slight modifications
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We provide here an unprecedented analysis of the three-dimensional re-organization of the genome during cellular reprograming of one cell type into another by the ectopic expression of one single transcription factor. By integrating Hi-C analysis with ChIPseq-based detection of MYOD genome-wide binding and RNAseq profiling of gene expression, we discovered that MYOD causes profound alterations in the high order chromatin structure during fibroblast reprogramming into skeletal muscle cells. We also used CTCF ChIPSeq in IMR90 GSE31477 (GSM935404); CTCF ChIPSeq in human myoblasts (hMB) GSE29611 (GSM733762);  CTCF ChIPSeq human myotubes (hMT) GSE29611 (GSM733783); H3K27Ac in IMR90 GSE43070 (GSM1055818); H3K27Ac in hMB GSE29611 (GSM733755); H3K27Ac in hMT GSE29611 (GSM733666) Same number of reads was used for H3K27Ac ChIP comparison. ChIPSeq p300 IMR90 GSE43070 (GSM1055812). We also used RNASeq from GSE90895 (GSM2417196, GSM2417197, GSM2417198, GSM2417204, GSM2417203) Overall design: Integration of RNASeq, ChIPSeq and HiC experiments to characterize the 3D regulatory mechanisms for the myogenic conversion of fibrobalsts. For this project we used CTCF ChIPSeq in IMR90 GSE31477 (GSM935404); CTCF ChIPSeq in human myoblasts (hMB) GSE29611 (GSM733762);  CTCF ChIPSeq human myotubes (hMT) GSE29611 (GSM733783); H3K27Ac in IMR90 GSE43070 (GSM1055818); H3K27Ac in hMB GSE29611 (GSM733755); H3K27Ac in hMT GSE29611 (GSM733666) Same number of reads was used for H3K27Ac ChIP comparison. We also used RNASeq from GSE90895 (GSM2417196, GSM2417197, GSM2417204, GSM2417203)
SAMPLE_TITLE: HiC_IMR90_MYOD_DM_Rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "IMR90"}, {"TAG": "cell type", "VALUE": "Lung fibroblast-derived myotube"}, {"TAG": "ectopic gene expression", "VALUE": "mouse MYOD overexpression"}, {"TAG": "passage from isolation", "VALUE": "passage 21-28"}]
Pool_Member_@attributes_sample_title: HiC_IMR90_MYOD_DM_Rep1
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