|
| Status |
Public on Apr 06, 2020 |
| Title |
GM12878-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
human B lymphocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
treatment: UV irradiation
time point (after treatment): 1 hour
replicate: 1
|
| Treatment protocol |
Cells grown to ~80% confluency in 15-cm plates were harvested 1 h and 5 minutes after irradiation with 20 J/m2 of UV.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples are pooled, lysed, and immunoprecipitated with anti-TFIIH antibodies p62 (Santa Cruz Biotechnology, sc292) and p89 (XPB, Santa Cruz Biotechnology, sc293).
Ligated to adapters and processed for sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
UV irradiated cell line derived from human B lymphocytes
|
| Data processing |
Library strategy: XR-Seq
3' adapter sequences trimmed using Cutadapt (Martin 2011) for XR-Seq reads
Reads were aligned to hg19 human genome and Mmur_3.0 mouse lemur genome with Bowtie2 version 2.3.4.1 (Langmead and Salzber 2012) with default parameters for XR-Seq reads.
Reads were aligned to hg19 human genome and Mmur_3.0 mouse lemur genome with Star version 2.6.1a (Dobin et al. 2012) with default parameters for RNA-Seq reads.
Aligned reads transformed to bed format, and sorted to remove duplicate reads
Genome_build: hg19 for human genome and Mmur_3.0 for mouse lemur
Supplementary_files_format_and_content: bed files containing regions and read counts
|
| |
|
| Submission date |
Feb 25, 2020 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Ogun Adebali |
| E-mail(s) |
oadebali@sabanciuniv.edu
|
| Organization name |
Sabanci University
|
| Department |
Mol. Bio. Genetics & Bioeng.
|
| Lab |
Adebali Lab
|
| Street address |
Orta Mahalle, Üniversite Caddesi No:27 Tuzla, Sabancı Üniversitesi
|
| City |
Istanbul |
| ZIP/Postal code |
34956 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE145883 |
Comparative analysis of genome-wide UV repair events in two primates show different rates but similar distribution. |
|
| Relations |
| BioSample |
SAMN14180204 |
| SRA |
SRX7798781 |
