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| Status |
Public on May 07, 2020 |
| Title |
pooled HiC |
| Sample type |
SRA |
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| Source name |
human coronary artery smooth muscle cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: smooth muscle cells
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| Treatment protocol |
not applicable
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| Growth protocol |
Primary human coronary artery smooth muscle cells (HCASMCs) derived from normal human donor hearts were purchased from three different manufacturers, Lonza, PromoCell and Cell Applications (all tested negative for mycoplasma contamination) at passage 2 and were maintained in growth-supplemented smooth muscle basal media (Lonza # CC-3182) according to the manufacturer’s instructions. All experiments were performed on HCASMCs between passages 4 and 7.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
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.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
1238 1278 1346 1347 1369 1386 1401 1448 1483 1497 1508 1522 1559 1576 1587 1596 1795 1848 1858 1923 2102 2105 2109 2115 2139 2228 2282 2305 2135 2356 2435 2510 2989 2999 3141 10705 20805 112201 177089 200212 289727 313605 317155 1020301 1042702 1060602 1062201.3 2030801 2040401 3100203 3101801 61646600 7103002 8072501 8100901 9052004 9070202 9071501 9092401 9102101 59386145 59885590 397Z030 399Z015 400Z012
4-7
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| Data processing |
Pooled HiC paired-end reads were aligned to the HCASMC phasing data masked hg19 genome using the HiC-Pro pipeline. Default settings were used to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices. Aligned reads were assigned to a specific allele on the basis of phasing data.
HiC-Pro filtered reads were then processed using the hicpro2juicebox and hicpro2fithic functions.
FitHiC and HiCCUPS ware used to identify high-confidence loops using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: HIC, TEXT, BEDPE
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| Submission date |
Dec 10, 2019 |
| Last update date |
May 07, 2020 |
| Contact name |
Thomas Quertermous |
| E-mail(s) |
tomq1@stanford.edu
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| Phone |
650-723-5012
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| Organization name |
Stanford University
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| Department |
Medicine Cardiology
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| Lab |
Quertermous
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| Street address |
300 Pasteur Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE141749 |
Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci (Hi-C) |
| GSE141752 |
Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci |
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| Relations |
| BioSample |
SAMN13523053 |
| SRA |
SRX7299331 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4212721_FitHiC_allloops.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSM4212721_FitHiC_filterloops.txt.gz |
144.4 Kb |
(ftp)(http) |
TXT |
| GSM4212721_G1_loops.hic |
121.2 Mb |
(ftp)(http) |
HIC |
| GSM4212721_G2_loops.hic |
121.2 Mb |
(ftp)(http) |
HIC |
| GSM4212721_HiCCUPS_allloop.bedpe.gz |
684.8 Kb |
(ftp)(http) |
BEDPE |
| GSM4212721_HiCCUPS_filterloop.bedpe.gz |
209.4 Kb |
(ftp)(http) |
BEDPE |
| GSM4212721_all_loops.hic |
1.2 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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