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Sample GSM3304265 Query DataSets for GSM3304265
Status Public on Feb 18, 2019
Title HIC_library_CBL0137-treated_replicate2
Sample type SRA
 
Source name connective tissue
Organism Homo sapiens
Characteristics tissue: HT1080 cells
disease: fibrosarcoma
oncogene: ras +
Treatment protocol Exposure of cells to CBL0137 (3 μm final concentration in the culture medium) was for 6 h.
Extracted molecule genomic DNA
Extraction protocol Hi-C was performed in two biological replicates using the DpnII restriction endonuclease according to a previously published protocol(Lieberman-Aiden Et al. 2009 (PMID: 19815776);Belton Et al. 2012(PMID: 22652625 )).Each Hi-C library was sequenced using paired end sequencing on an Illumina HiSeq 3000 in two technical replicates;
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina HiSeq 3000
 
Data processing Reads for each biological replicate were pooled and mapped to the human genome (version hg19) using hiclib(Imakaev Et al. 2012(PMID: 22941365 )) (https://bitbucket.org/mirnylab/hiclib/).
Reads mapped in close proximity to DpnII restriction sites (5 bp), reads mapped on the same fragment, and possible PCR duplicates were eliminated. Resulting pairs were binned into 20 Kb genomic windows, and contact maps were generated.
Contact maps were iteratively corrected(Imakaev, 2012) using cooler (https://github.com/mirnylab/cooler)
Genome_build: hg19
Supplementary_files_format_and_content: cool files were generated using cooler version 0.7.9
 
Submission date Jul 24, 2018
Last update date Feb 18, 2019
Contact name Artem Luzhin
E-mail(s) artyom.luzhin@gmail.com
Organization name Institute of Gene Biology RAS
Street address Vavilova 34/5
City Moscow
ZIP/Postal code 119334
Country Russia
 
Platform ID GPL21290
Series (2)
GSE117582 Anti-cancer drugs curaxins target the 3D genome organization [HiC]
GSE122463 Anti-cancer drugs curaxins target the 3D genome organization
Relations
BioSample SAMN09708994
SRA SRX4452175

Supplementary file Size Download File type/resource
GSM3304265_CBLtreated2_20000.cool.gz 84.7 Mb (ftp)(http) COOL
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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