Computational protocol: Phenotypically distinct helper NK cells are required for gp96-mediated anti-tumor immunity

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Protocol publication

[…] Adaptor sequences and low quality reads were trimmed using Fastq Trimmer. Reads were mapped to the murine reference genome (mm9) using TopHat software package and annotation of known Ensembl transcripts was obtained from Illumina igenomes on the Galaxy database. FPKM values were calculated with Cufflinks and differentially expressed genes were analyzed using Cuffdiff. Genetrail was used for gene ontology analysis to test for enrichment of gene families associated with differentially expressed genes. We performed this analysis using default parameters set by Genetrail software and show enrichment results requiring 5+ genes per family. […]

Pipeline specifications

Software tools TopHat, Galaxy, Cufflinks, GeneTrail
Databases iGenomes
Application RNA-seq analysis
Diseases Carcinoma, Renal Cell, Neoplasms