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Sample GSM2795535 Query DataSets for GSM2795535
Status Public on Oct 05, 2017
Title Rao-2017-HIC001
Sample type SRA
Source name Colorectal carcinoma
Organism Homo sapiens
Characteristics cell line: HCT-116-RAD21-mAC
protocol: in situ Hi-C
tissue: Colorectal carcinoma
Growth protocol Cell lines were cultured according to manufacturer's instructions
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten following the manufacturer's protocols
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model HiSeq X Ten
Data processing The paired end reads were aligned separately using BWA against the b37 human build
PCR duplicates, low mapping quality and unligated reads were removed using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Contact matrices were constructed at various resolutions and normalized using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
loops were annotated using HiCCUPS (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016), domains were annotated using Arrowhead (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Genome_build: b37 (human)
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions in an easy to visualize and access format) (see Durand, Robinson, et al Cell Systems 2016)
Submission date Sep 27, 2017
Last update date May 15, 2019
Contact name Suhas Rao
Organization name Baylor College of Medicine
Department Molecular and Human Genetics
Lab The Center for Genome Architecture
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platform ID GPL20795
Series (2)
GSE104333 Cohesin loss eliminates all loop domains [HiC]
GSE104334 Cohesin loss eliminates all loop domains
BioSample SAMN07710785
SRA SRX3222724

Supplementary file Size Download File type/resource
GSM2795535_Rao-2017-HIC001.hic 7.8 Gb (ftp)(http) HIC
GSM2795535_Rao-2017-HIC001_30.hic 7.3 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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