Computational protocol: Interaction of tankyrase and peroxiredoxin II is indispensable for the survival of colorectal cancer cells

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Protocol publication

[…] Four samples of the siRNA-transfected HT29 cells were prepared for high-throughput mRNA sequencing. Total RNA of 1 μg was extracted from each sample and the mRNA library (insert size of ~300 bp) was created using the TruSeq RNA Library Preparation kit v2 (Illumina). Paired-end transcriptome sequencing (101 bp read length) was performed on Illumina HiSeq 2500. The number of reads for each sample ranged from 69.4 million to 74.8 million. The raw sequencing data were deposited in the GEO database (Accession Number: GSE81429). RNA-Seq data were aligned to the human genome (hg19 from UCSC) using MapSplice v2.1.7 after standard quality check and trimming with FastQC and Fastx-toolkit, respectively. The mapping rate of reads was between 96.5 and 96.8%. RSEM v1.2.12 was used to estimate the transcriptome abundance for refGene mRNAs. Differentially expressed genes were identified using DESeq2 with the FDR cutoff of 0.05. […]

Pipeline specifications

Software tools MapSplice, FastQC, FASTX-Toolkit, RSEM, DESeq2
Databases RefGene
Application RNA-seq analysis
Organisms Homo sapiens, Mus musculus
Diseases Neoplasms, Adenomatous Polyposis Coli, Colorectal Neoplasms
Chemicals Poly Adenosine Diphosphate Ribose