Computational protocol: Post-Transcriptional Regulation of KLF4 by High-Risk Human Papillomaviruses Is Necessary for the Differentiation-Dependent Viral Life Cycle

Similar protocols

Protocol publication

[…] RNA-sequencing was performed using Illumina HiSeq 2500 NGS platform. Sequencing data were used as input to CRI Illumina RNA-seq pipeline for quality control assessment of raw sequencing data, reads mapping, post-alignment QC, expression quantification, and DEGs identification. The quality of raw sequencing reads was assessed using FastQC v0.11.2, and the post-alignment QC was evaluated with RSeQC v2.3.9[] and Picard tools v1.117. Reads were mapped to 1). UCSC human genome (hg19) obtained from GATK resource bundle v2.8 using TopHat v2.0.13 [] guided with UCSC gene annotation model (hg19) obtained from Illumina iGenomes, and 2) HPV31 virus genome with GenBank accession number J04353.1. Gene transcripts were assembled and quantified on human and HPV31 genome separately using Cufflinks v2.2.1 [] with the hg19 UCSC gene model annotation and HPV31 RefSeq gene annotation as a guide respectively for transcript assembly and bias detection/correction. Sample-based assemblies were merged together using Cuffmerge wrapped in Cufflinks v2.2.1 before quantification of transcripts using Cufflinks wrapped method Cuffnorm and count-based method featureCounts[]. DEGs were identified between 4 various group comparisons using Cuffdiff wrapped in Cufflinks v2.2.1. During the entire analysis, R (R Core Team, 2014) were used to assist in the exploration and summarization of the analysis results. […]

Pipeline specifications

Software tools FastQC, RSeQC, Picard, GATK, TopHat, Cufflinks, Subread
Databases iGenomes
Application RNA-seq analysis
Organisms Homo sapiens, Viruses, Human papillomavirus