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Sample GSM2522825 Query DataSets for GSM2522825
Status Public on Jun 04, 2020
Title HCT116_PolyA_seq_2
Sample type SRA
 
Source name HCT117 cells
Organism Homo sapiens
Characteristics cell type: human colon cancer cells
cell line: HCT116
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol and treated with RQ1 DNase (Promega) to remove DNA
Total RNA was partially fragmented with RNase T1. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads. 3’ adaptor was added to purified mRNAs, followed by reverse transcription performed with RT primer harboring 5' adaptor sequence and randomized hexamer. The cDNAs were purified and PCR amplified for library construction for Illumina NextSeq 500 system.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing NextSeq Control Software 1.4 was used for basecalls.
Reads were trimmed for polyG sequence, and polyA sequence shorter than 11nt were discarded. PolyA lengths were counted from basecalls.
Sequenced reads were trimmed for polyA and adaptor sequence, and reads longer than 20nt were mapped to GRCH38 whole genome using tophat2 with parameters -a 8 -m 0 -g 2 --microexon-search --report-secondary-alignments --read-edit-dist 4 N 2 --b2-N 1
the median of polyA sequence length was calculated of each gene.
Genome_build: GRCH38
Supplementary_files_format_and_content: txt file, the median of polyA length of each gene in each sample
 
Submission date Mar 06, 2017
Last update date Jun 04, 2020
Contact name Dong Chen
Organization name ABLife, Inc.
Department Center for Genome Analysis
Street address 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
City Wuhan
State/province Hubei
ZIP/Postal code 430075
Country China
 
Platform ID GPL18573
Series (1)
GSE84287 A novel method for genome-wide profiling of poly(A)-tail lengths
Relations
BioSample SAMN06481593
SRA SRX2614230

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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