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Sample GSM2522821

Query DataSets for GSM2522821

Status

Public on Jun 04, 2020

Title

si-PTB_PolyA_seq_2

Sample type

SRA

Source name

HeLa cells

Organism

Homo sapiens

Characteristics

cell type: human cervical cancer cells
cell line: HeLa

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