Computational protocol: Hexokinase 2 promotes tumor growth and metastasis by regulating lactate production in pancreatic cancer

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Protocol publication

[…] 200-1000 ng of total RNA was used to prepare libraries with the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA, USA). 75 bp paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina). Reads were separated by species of origin using Xenome []. Human specific reads were then aligned and quantified using Tophat2 [], Cufflinks [], hg19, mm10, and the UCSC transcript and gene definitions (genome.ucsc.edu). mRNA gene expression was analyzed with javaGSEAv2.2.1, and MSigDBv5.0 []. […]

Pipeline specifications

Software tools Xenome, TopHat, Cufflinks
Application RNA-seq analysis
Organisms Mus musculus, Homo sapiens
Diseases Neoplasms, Pancreatic Neoplasms, Carcinoma, Pancreatic Ductal
Chemicals Glucose, Lactic Acid