EXPERIMENT_TITLE: GSM4212721: pooled HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: The cells were washed with PBS and then harvested in Hi-C lysis buffer (10 mM Tris-HCl, pH 8, 10 mM NaCl, 0.2 % NP-40). Nuclei pellet was incubated in 0.5% SDS at 62 °C for 10 min and then quenched by water and 10% Triton X-100. MboI (NEB, R0147) enzyme digested DNA for 2 hours at 37 °C. Biotin labeled dATP (Thermo,19524016) and Klenow (NEB, M0210) were used to fill restriction fragment overhangs. The DNA was re-ligated by T4 DNA ligase (NEB, M0202) at room temperature for 4 hours. Re-ligated nuclei were lysis by 0.5% SDS and sheared for 2 min by sonication before extensive centrifugation. Supernatant was incubated at 65 °C over-night with Protease K and the DNA was purified. For libraries construction, set aside DNA by 150 ng to the biotin capture step. Biotin labeled DNA was pre-bound to Streptavidin C-1 beads (Thermo, 65-001) in biotin binding buffer. After Tween buffer and TD buffer washing, Tn5 transposition was performed on beads at 55 °C for 10 min. Libraries were generated by PCR amplification with Nextera adapters added after washing the beads. Samples were size selected by PAGE purification (300–700 bp) for effective paired end sequencing and adapter dimer removal.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To better understand the fundamental molecular mechanisms that contribute to complex human diseases such as coronary artery disease (CAD), we have created a catalog of genetic variants associated with three stages of transcriptional cis-regulation in primary human coronary artery vascular smooth muscle cells. To this end, we used a pooling approach to map quantitative trait locus associations (QTLs) for TCF21 binding (ChIPseq), chromatin accessibility (ATACseq), and chromosomal looping (HiC). We find significant overlap of these QTLs, and several analyses indicate their relationship to smooth muscle specific genes, the binding of smooth muscle transcription factors, and enrichment in CAD-associated loci. These QTLs are extensively validated and allele-specific chromatin  looping at the FN1 disease locus is shown to be mediated by activation of the CAD-associated TGFb1 pathway. In sum, these results uncover thousands of loci affecting cis-regulation in a key cell type for CAD, including many that may contribute to CAD risk. Overall design: Human coronary artery smooth muscle cells (HCASMC) grown in serum.Approximately 97.5M HCASMC, 1.5M from 65 different cell lines were pooled and fixed with 1 % formaldehyde and quenched by glycine.
SAMPLE_TITLE: pooled HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human coronary artery smooth muscle cells"}, {"TAG": "cell type", "VALUE": "smooth muscle cells"}]
Pool_Member_@attributes_sample_title: pooled HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: pooled HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Pooled_HiC_1.fq.gz", "size": "53997288120", "date": "2019-12-11 05:08:32", "md5": "914459f724a92894771f3e4c9d2219f9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Pooled_HiC_2.fq.gz", "size": "57138885237", "date": "2019-12-11 04:23:10", "md5": "c70640250932e360a9dfaaf27807bd31", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR10620237", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10620237/SRR10620237", "size": "67999751528", "date": "2019-12-11 06:21:29", "md5": "7ff2cbbd618ff06bc5230ebfd1d52ab7", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR10620237.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR010/10620/SRR10620237/SRR10620237.lite.1", "size": "44853145892", "date": "2022-07-21 17:11:21", "md5": "b827c7fb2664de64e67aaacdb87e951d", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]