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Sample GSM3791905

Query DataSets for GSM3791905

Status

Public on Dec 22, 2019

Title

BGI EC109 shAR1 #9

Sample type

SRA

Source name

human esophageal squamous carcinoma cells

Organism

Homo sapiens

Characteristics

cell type: human esophageal squamous carcinoma cells
treatment: ADAR1 knockdown

Treatment protocol

Human ESCC cells were treated with specific shRNAs for silecing ADAR1/2 or transfected with expression construct for overexpressing ADAR1/2.

Growth protocol

Extracted molecule

total RNA

Extraction protocol

Total RNA samples were extracted using Qiagen Rneasy Mini Kit.
Strand-specific cDNA library according to Illumina's TruSeq Stranded mRNA Library Prep Kit.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Description

strand-specific RNA-Seq

Data processing

Reads with adapters, unknown bases more than 10% and low quality bases (<=5) more than 50% were removed using SAOPnuke software.
Read mapping was performed by using STAR (v2.5) with the reference human genome version 19 (hg19) as the annotation library.
For the splicing analysis, mapped reads were filtered and classified into the following three groups based on their distance and location around the annotated splice sites: 1) reads mapped to exon-exon junctions, 2) reads bridging exon-intron junctions, and 3) reads mapped completely to introns.
The reads in Group 3 were used for intron retention coverage and depth calculations. The reads in Groups 1 and 2 were used for the calculation of splicing index (SI) for each splice site for the selection of potential differential splicing candidates.
To identify the various types of splicing events including exon skipping, intron retention and alternative splice sites, the SI calculation was adjusted for each type of splicing events.
All potential splicing candidates were classified into either known/annotated alternative splicing or novel splicing events that are not represented in the annotation library, and were assessed by Fisher’s exact test and SI change.
For this study, only candidates with total junction reads≥15, |ΔSI| ≥ 10% with a FDR<0.2 in the opposite direction of change for KD and OE samples were selected.
Genome_build: hg19
Supplementary_files_format_and_content: spreadsheet file include ADAR1 or ADAR2 knockdown or overexpression specific high confidence alternative splicing events (intron retention, casette exon and alternative splice site)

Submission date

May 22, 2019

Last update date

Dec 22, 2019

Contact name

Polly Leilei Chen

E-mail(s)

polly_chen@nus.edu.sg

Phone

+6565168435

Organization name

Cancer Science Institute of Singapore NUS