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Sample GSM2247306 Query DataSets for GSM2247306
Status Public on Jun 25, 2017
Title HiC Primary Epidermal Keratinocyte Biological Replicate 1 - Differentiation Day 3
Sample type SRA
 
Source name Primary Epidermal Keratinocyte - Differentiation Day 3
Organism Homo sapiens
Characteristics cell type: primary epidermal keratinocyte
differentiation state: Early Differentiation (Day 3)
individual: Donor1
Sex: male
restriction enzyme: HindIII
Treatment protocol None
Growth protocol Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiated for three or six days as previously described (Zarnegar et al., 2012)
Extracted molecule genomic DNA
Extraction protocol Cells were cross-linked in 2% formaldehyde for 10 min at RT and flash frozen. After digestion of nuclei with HindIII, DNA ends were labeled with biotin-14–dATP (Life Technologies) in a Klenow end-filling reaction and ligated in nuclei overnight. DNA was sheared, end repaired, A-tailed and subjected to pull down with streptavidin beads.
Paired-end adaptors were ligated (Illumina) and libraries were PCR-amplified and either sequenced directly or enriched for promoter fragments with RNA oligonucleotide baits.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description Sample 2
Processed data file(s): HiC_matrices_norm_Day3.tar.gz
Data processing Library strategy: HiC-Seq
Sequencing reads were aligned and paired, filtered for valid long-range contacts, and removed of duplicates using the HiCUP pipeline.
The CHiCAGO tool was used to identify signicant contacts between captured baits on other fragments at an FDR < 0.01.
Bait to bait interactions (b2b) reaching FDR < 0.01 on any of Day 0, Day 3, or Day 6 are included with supporting read counts from each replicate.
Bait to non-bait (or bait to "genome") interactions (b2g) reaching FDR < 0.01 and associated with an H3K27ac peak on any of Day 0, Day 3, or Day 6 are included with supporting read counts from each replicate.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file reports one contact per row. Interacting HindIII fragments are represented in bed format (chr/start/stop) with bait (or upstream bait, in the case of b2b contacts) listed first. The following fields correspond to a unique contact ID, fragment IDs for first and second fragments, and raw read counts supporting contacts in each replicates.
 
Submission date Jul 21, 2016
Last update date May 15, 2019
Contact name Paul Khavari
Organization name Stanford University
Street address 269 Campus Drive, CCSR 2150
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL11154
Series (2)
GSE84660 Dynamic and stable enhancer-promoter contacts regulate terminal differentiation [HiC_CHiC]
GSE84662 Dynamic and stable enhancer-promoter contacts regulate terminal differentiation
Relations
BioSample SAMN05425775
SRA SRX1967826

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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