|
| Status |
Public on Jun 25, 2017 |
| Title |
HiC Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 0 |
| Sample type |
SRA |
| |
|
| Source name |
Primary Epidermal Keratinocyte - Differentiation Day 0
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary epidermal keratinocyte
differentiation state: Undifferentiated (Day 0)
individual: Donor2
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 4
Processed data file(s): HiC_matrices_norm_Day0.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 |
SAMN05425801 |
| SRA |
SRX1967828 |
