|
| Status |
Public on Jun 25, 2017 |
| Title |
UMI-4C Primary Epidermal Keratinocyte Biological Replicate 2 - Differentiation Day 3 - EHF siRNA |
| Sample type |
SRA |
| |
|
| Source name |
Primary Epidermal Keratinocyte - Differentiation Day 3 - EHF siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary epidermal keratinocyte
differentiation state: Differentiated (Day 3)
Sex: male
genotype/variation: EHF knockdown
|
| Treatment protocol |
Progenitor keratinocytes were nucleofected with scrambled control, KLF4, ZNF750, or EHF targeting siRNAs
|
| 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. Nuclei were digested with MboI and ligated in nuclei overnight.
UMI-4C universal adapter was ligated and custom two-step bait primers were used for library PCR.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Sample 10
|
| Data processing |
Sequencing reads were aligned and paired, filtered for valid long-range contacts, and removed of duplicates using the HiC-Pro pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited BED 6 file contains processed read counts supporting contact between two 5kb regions of the genome.
Column 1: Bin #1 - chromosome
Column 2: Bin #1 - start position
Column 3: Bin #1 - end position
Column 4: Bin #2 - chromosome
Column 5: Bin #2 - start position
Column 6: Bin #2 - end position
Column 7: HiC-Pro filtered read counts
|
| |
|
| Submission date |
Feb 20, 2017 |
| 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 |
GPL20301 |
| Series (2) |
| GSE84662 |
Dynamic and stable enhancer-promoter contacts regulate terminal differentiation |
| GSE95098 |
Dynamic and stable enhancer-promoter contacts regulate terminal differentiation [UMI-4C] |
|
| Relations |
| BioSample |
SAMN06349998 |
| SRA |
SRX2577860 |
