|
| Status |
Public on Jul 20, 2018 |
| Title |
5GY-IGG |
| Sample type |
SRA |
| |
|
| Source name |
WS1 cell
|
| Organism |
Homo sapiens |
| Characteristics |
tissue origin: skin
cell line: WS1
cell type: fibroblast cell
treated with: single dose of 5 Gy X-ray irradiation
time point: 24h after irradiation
rip antibody: IgG (abcam, lot:ab172730)
|
| Treatment protocol |
24h after a single dose of 5 Gy X-ray irradiation,cells were harvested
|
| Growth protocol |
WS1 cell was cultured with DMEM (10%FBS)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction protocol: total RNA was extracted from the RIP assay products using Trizol (Invitrogen,USA). All samples passed the control analysis
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded Total RNA Library Prep Kit (Illumina,USA)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
RIP-seq reads were adaptor-trimmed and mapped to human genome (hg19) by bowtie2 software with default parameters.
Peak calling was performed with MACS software (v1.4.3). Differentially enriched regions were identified by diffReps software (v1.55.4).
Genome_build: hg19
Supplementary_files_format_and_content: bed
|
| |
|
| Submission date |
Aug 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
shuyu zhang |
| E-mail(s) |
mathhavs@hotmail.com
|
| Phone |
15851417273
|
| Organization name |
Soochow University
|
| Street address |
199 Ren'ai Road
|
| City |
Suzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
215123 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE102146 |
RIP-sequencing reveals that X-ray irradiation infection ELAVL1 binding RNA sites |
| GSE102147 |
High throughput sequencing of human fibroblast WS1 cells after 5 Gy X-ray irradiation |
|
| Relations |
| BioSample |
SAMN07437173 |
| SRA |
SRX3055077 |
