Computational protocol: The novel 19q13 KRAB zinc-finger tumour suppressor ZNF382 is frequently methylated in oesophageal squamous cell carcinoma and antagonises Wnt/β-catenin signalling

Similar protocols

Protocol publication

[…] RNA-Seq was performed by the Novogene Bioinformatics Technology Company (Beijing, China). RNA integrity was assessed with an RNA Nano 6000 Assay Kit included with the Bioanalyzer 2100 system (Agilent Technologies, CA). Sequencing libraries were prepared using a NEBNext Ultra RNA LibraryPrep Kit for Illumina (New England Biolabs) following the manufacturer’s recommendations. RNA-Seq was performed with an Illumina Hiseq 2000/2500 platform. Bowtie v. 2.0.6– and TopHat v. 2.0.9– were used for reads mapping to the reference genome. Genes with an adjusted p or0.05 and identified with DESeq, were considered to be differentially expressed. […]

Pipeline specifications

Software tools Bowtie, TopHat, DESeq
Application RNA-seq analysis
Diseases Carcinoma, Squamous Cell, Esophageal Neoplasms, Neoplasms
Chemicals Zinc