EXPERIMENT_TITLE: GSM4340725: Hi-C Msc Experiment #1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed using in-nucleus ligation following a modified version of a previously described protocol (Nagano et al., 2015). Chromatin was digested using MboI restriction enzyme. The digested ends were filled in using biotinylated d-ATP and ligated. Chromatin was de-crosslinked and purified by phenol-chloroform extraction. Purified DNA (50 µg) was sheared to an average size of 400 bp by sonication (Covaris). The sheared DNA was end-repaired, adenine-tailed and double size-selected using AMPure XP beads to isolate DNA ranging from 250 to 550 bp. Ligation fragments marked by biotin were immobilized using MyOne Streptavidin C1 DynaBeads (Invitrogen) and ligated to NEBNext hairpin adaptors (New England Biolabs) followed by U excision by USER Enzyme (New England Biolabs). The resulting Hi-C libraries were amplified using universal primer and 6bp-index primers (New England Biolabs). Hi-C libraries were constructed from genomic DNA according to the manufacturer's instructions (Illumina).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Adipocyte differentiation is driven by waves of transcriptional regulators that reprogram the en-hancer landscape and change the wiring of the promoter interactome. Here, we establish enhancer-capture Hi-C to interrogate the extent and role of enhancer-to-enhancer interactions during adi-pocyte differentiation of human mesenchymal stem cells. We find that enhancers form an elaborate network that is highly dynamic during differentiation and tightly coupled to changes of enhancer activity. These interactions are important for enhancer function, since transcription factors at baited enhancers stabilize transcription factor binding at target enhancers, a phenomenon we term cross-interaction stabilization of transcription factors (CIST). Moreover, highly interconnected enhancers (HICE) act as integration hubs orchestrating differentiation by formation of insulated 3D enhancer communities, inside which, HICE, and other enhancers, converge on phenotypically important gene promoters. Collectively, these results indicate that dynamic enhancer interactions play a key role in regulation of enhancer function, and that HICE are important for both signal integration and compartmentalization of the genome. Overall design: Genome-wide profiling of transcription factors using ChIP-seq, gene expression using RNA-seq and enhancer-anchored chromatin interactions using enhancer capture Hi-C during adipocyte differentiation of human mesenchymal stem cells.
SAMPLE_TITLE: Hi-C Msc Experiment #1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "BM-hMSC-TERT4"}, {"TAG": "cell type", "VALUE": "Stem cell"}, {"TAG": "Stage", "VALUE": "Day 0"}]
Pool_Member_@attributes_sample_title: Hi-C Msc Experiment #1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C Msc Experiment #1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR11186852.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR011/11186/SRR11186852/SRR11186852.lite.1", "size": "22420048001", "date": "2022-06-22 15:14:47", "md5": "4712ff13836d43d00caec2b82b3b3f7e", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR11186852", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11186852/SRR11186852", "size": "27037689245", "date": "2020-02-26 20:33:05", "md5": "9c34ab37783b962c0dec96fe040df641", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_Msc_E1_SM2629_R2.fq.gz", "size": "21889384568", "date": "2020-02-26 19:41:28", "md5": "522cb179cb1c28e8e4fe3cbdae222f85", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_Msc_E1_SM2629_R1.fq.gz", "size": "20581665849", "date": "2020-02-26 19:06:09", "md5": "91ec223207117402c7833811cadd7fca", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]