|
| Status |
Public on Jun 25, 2017 |
| Title |
CTCF ChIP-seq Primary Epidermal Keratinocyte - 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: Donors not specified for single biological replicate experiments
Sex: male
chip antibody: CTCF (Millipore, catalog# 07-729, lot# JBC1881349)
|
| Treatment protocol |
In the case of siRNA knockdown, 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 crosslinked with 1% formaldehyde for 10 minutes, then quenched with 0.125M glycine for 5 minutes. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with an antibody.
NEB Next ChIP-seq library prep kit was used.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 7
|
| Data processing |
Reads were aligned with bowtie2 using default parameters.
Aligned reads were filtered for MAPQ > 30 and deduplicated with samtools.
Signal tracks were generated by first using the bedtools genomeCoverageBed to produce bedGraph files.
The UCSC utility bedGraphToBigWig was used with default parameters to generate bigwig files.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for each ChIP experiment are in UCSC format.
|
| |
|
| 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 |
GPL16791 |
| Series (2) |
| GSE84657 |
Dynamic and stable enhancer-promoter contacts regulate terminal differentiation [ChIP-Seq] |
| GSE84662 |
Dynamic and stable enhancer-promoter contacts regulate terminal differentiation |
|
| Relations |
| BioSample |
SAMN05425730 |
| SRA |
SRX1967776 |
