|
| Status |
Public on Apr 11, 2017 |
| Title |
K3D, UV, 72h/30 mJ/cm2 (time/dose)_Exome-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
|
| 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 |
Genomic DNA was isolated from UV-irradiated and control samples using the Wizard Genomic DNA Purification Kit (Promega).
Exome-Seq was performed at the Columbia Genome Center following standard Illumina TruSeq multiplexing protocol to generate targeted number of reads with more than 85% coverage of the targeted regions by ≥15 reads and 90% covered by ≥10 reads.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: K3DvsK0_EXOMESEQ.vcf
|
| Data processing |
Library strategy: Exome-Seq
For Exome-Seq, reads were mapped to the NCBI/build37.2 genome using the BWA algorithm. Mapped reads were sorted and indexed using the Samtools program. UV-induced somatic mutations between the paired UV-4h vs. control or UV-72h vs. control were called using Samtools mpileup and bcftools.
genome build: NCBI/build37.2
processed data files format and content: For Exiome-Seq, vcf files include the genetic variants that are different between the UVR-treated versus no-UVR control samples.
|
| |
|
| 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 |
GPL11154 |
| Series (1) |
| GSE97577 |
Epigenetic and genetic dissections of UV-induced global gene dysregulation in skin cells through multi-omics analyses |
|
| Relations |
| BioSample |
SAMN06704794 |
| SRA |
SRX2731740 |
