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Sample GSM1184323 Query DataSets for GSM1184323
Status Public on Aug 13, 2013
Title Hi-C Tcell Rad21WT R1
Sample type SRA
 
Source name CD4+ CD8+ Double Positive Thymocytes
Organism Mus musculus
Characteristics cell type: CD4+ CD8+ Double Positive Thymocytes
genotype: Rad21 KO
genetic background: C57BL\6 and 129 mixed
Extracted molecule genomic DNA
Extraction protocol Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: A comprehensive technique to capture the conformation of genomes. Methods. 2012 Nov; 58(3):268-76.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer II
 
Data processing DEKKER ICE METHOD - all relevant HiC data (binned at 4 resolutions) raw + iced data
UCSC GENOME BROWSER BED FILE - coordinates of all chip-seq peaks
Tab delmited file of all gene expression values (count equivalents) across all 4 samples.
Genome_build: mm9
Supplementary_files_format_and_content: peak bed (ChIP-seq), counts (RNA-Seq), and HiC data
 
Submission date Jul 10, 2013
Last update date May 15, 2019
Contact name Andre J Faure
E-mail(s) andre.faure@crg.eu
Organization name Centre for Genomic Regulation (CRG)
Department EMBL-CRG Systems Biology Unit
Street address Dr. Aiguader 88
City Barcelona
ZIP/Postal code 08003
Country Spain
 
Platform ID GPL9250
Series (1)
GSE48763 Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments.
Relations
Reanalyzed by GSE87112
SRA SRX320075
BioSample SAMN02230619

Supplementary file Size Download File type/resource
GSM1184323_HiCMYZ-Tcell-Rad21WT-R1.mm9.NA.tar.gz 471.2 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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