|
| Status |
Public on May 01, 2016 |
| Title |
RKO_uv0.5h |
| Sample type |
SRA |
| |
|
| Source name |
RKO colon cancer cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: a poorly differentiated colon carcinoma cell line
cell line: RKO
treatment: UV 0.5h
|
| Treatment protocol |
Colon carcinoma RKO cells were treated with UV irradiation and allowed to recover for 0.5 hr or 2 hr.
|
| Growth protocol |
RKO cell lines were cultured in Eagle's minimal essential medium (EMEM) and Dulbecco’s modified Eagles medium (DMEM) respectively. Media were supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin antibiotic.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclear RNA was purified using the RNeasy kit (Qiagen) following manufacturer’s protocol.
Total RNA was processed by the 3’ READS method as previously described (Nat Methods. 2013 Feb;10(2):133-9.)
3'READS (a recently developed deep sequencing method for analysis of APA isoform expression genome-wide)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
nuclear RNA
|
| Data processing |
Basecalls performed using CASAVA (Illumina).
Reads were mapped to reference genome using bowtie2 (local mode)
The poly(A) site supporting (PASS) reads are those with unique alignment with the genome and having at least two extra 5’Ts (corresponding to the poly(A) sequence) after alignment.
Poly(A) sites identified by PASS reads were clustered if located within 24 nt from each other, and were further assigned to genes using the RefSeq information.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each pA
|
| |
|
| Submission date |
Aug 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiyeon Park |
| Organization name |
The Catholic University of Korea
|
| Department |
Catholic Center for Precision Medicine Research
|
| Street address |
222, Banpo-daero
|
| City |
Seoul |
| ZIP/Postal code |
06591 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE71801 |
U1 snRNP regulates alternative polyadenylation in DNA damage response |
|
| Relations |
| SRA |
SRX1135322 |
| BioSample |
SAMN03979434 |
