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Sample GSM1846071 Query DataSets for GSM1846071
Status Public on May 01, 2016
Title RKO_uv0.0h
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: baseline
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
E-mail(s) parkji7@snu.ac.kr
Organization name Seoul National Univerisy
Department Biomedical Informatics
Lab Bioinformatics
Street address 103 Daehak-ro, Jongno-gu
City Seoul
ZIP/Postal code 110-799
Country South Korea
 
Platform ID GPL9115
Series (1)
GSE71801 U1 snRNP regulates alternative polyadenylation in DNA damage response
Relations
SRA SRX1135321
BioSample SAMN03979433

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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