GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2861709 Query DataSets for GSM2861709
Status Public on Nov 24, 2017
Title T-cell_HiC
Sample type SRA
Source name CD3+
Organism Homo sapiens
Characteristics cell type: Human T-cells
cell surface marker: CD3+
Extracted molecule genomic DNA
Extraction protocol One to five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. After nuclei permeabilization, DNA was digested with MboI, and digested fragments were labeled using biotinylated d-ATP and ligated. After reverse crosslinking, ligated DNA was purified and sheared to a length of ∼400 bp and biotin labeled DNA fragments were pulled down with streptavidin beads and prepped for Illumina sequencing.
Sequencing libraries were constructed according to previous publication Science 326, 289-93 (2009)
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model HiSeq X Ten
Description HIC1255
Data processing All data was processed using Juicer (Durand et al.2016; Rao et al.2014)
Loops were annotated using HiCCUPS (Durand et al.2016; Rao et al.2014)
Files ending in '_inter_30.hic' were further processed to include only reads with a read quality score above 30
Genome_build: hg19
Supplementary_files_format_and_content: hic
Submission date Nov 20, 2017
Last update date May 15, 2019
Contact name Jianzhong Su
Phone 8322902241
Organization name Baylor college of Medicine
Street address 1 Baylor Plaza
State/province TEXAS
ZIP/Postal code 77030
Country USA
Platform ID GPL20795
Series (2)
GSE104579 DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells
GSE107148 DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [HiC]
BioSample SAMN08045400
SRA SRX3408797

Supplementary file Size Download File type/resource
GSM2861709_HIC1255_aligned_inter.hic 9.5 Gb (ftp)(http) HIC
GSM2861709_HIC1255_aligned_inter_30.hic 8.9 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap