|
| Status |
Public on Apr 11, 2017 |
| Title |
K3D, UV, 72h/30 mJ/cm2 (time/dose)_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
neonatal foreskin
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: neonatal foreskin
cell type: Cultured primary keratinocytes
treatment: UVR
uv dose (time/dose): 72h/30 mJ/cm2
chip antibody: H3K27ac HistonePath™ Kit (Active Motif)
|
| Treatment protocol |
Cells were irradiated in approximately 0.5 ml PBS in each 10 cm dish with 30 mJ/cm2 UV. Control and irradiated cells were collected at 4 or 72 hours after UV radiation.
|
| Growth protocol |
Primary human keratinocytes were isolated from neonatal foreskins and were cultured in 154CF medium supplemented with human keratinocyte growth supplement (Life Technologies, Grand Island, NY)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% (final concentration) freshly prepared formaldehyde at 37°C for 15 min. The fixation was stopped by incubation in 125 mM (final concentration) glycine solution for 5 min at RT. Cells were washed with PBS containing proteinase inhibitor cocktail (1x final concentration), scraped and collected as cell pellets in Eppendorf tubes.
ChIP assays and sequencing were performed by Active Motif using the H3K27ac HistonePath™ Kit following standard protocols (Active Motif, Carlsbad, CA)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
For Chip-Seq, reads generated by Illumina sequencing were mapped to the NCBI/build37.2 genome using the BWA algorithm. ChIP-Seq tags were extended at their 3’-ends to 200bp. The genome was divided into 32-nt bins to estimate the density of extended tags in each bin along the genome. The model-based analysis of ChIP-Seq (MACS) algorithm was used for peak calling to identify chromatin regions with H3K27Ac tags compared to the input control. Genes were annotated if peaks were within 10 kb of start or end of a nearby gene.
genome build: NCBI/build37.2
processed data files format and content: bigwig files contain genome wide chip-seq signals for a histone mark (H3K27Ac) that could be visualized in UCSC or IGV.
|
| |
|
| Submission date |
Apr 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Liang Liu |
| Organization name |
Columbia University
|
| Street address |
1150 St. Nicholas Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE97577 |
Epigenetic and genetic dissections of UV-induced global gene dysregulation in skin cells through multi-omics analyses |
|
| Relations |
| BioSample |
SAMN06704795 |
| SRA |
SRX2731737 |
