Computational protocol: CD215+ Myeloid Cells Respond to Interleukin 15 Stimulation and Promote Tumor Progression

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Protocol publication

[…] The sequencing reads were mapped to the mouse RefSeq-RNA reference sequence (downloaded from http://hgdownload.cse.ucsc.edu/downloads) using the FANSe 2 algorithm (available from http://bioinformatics.jnu.edu.cn/software/fanse2/) with the parameters −L85 −E3 −U0 −S1015. Alternative splice variants were merged. Genes with at least 10 mapped reads were considered to be reliably detected genes. These genes were further quantified using count values, which were raw counts of sequencing reads. The count values were imported into the DESeq software package to calculate the up/downregulation of genes among untreated CD215− cells, untreated CD215+ cells, CD215− cells treated with IL-15, and CD215+ cells treated with IL-15. For the RNA-Seq analysis, all count values of mouse genes with more than a twofold change were imported into the DAVID database (available from http://david.abcc.ncifcrf.gov/home.jsp). The up- or downregulated genes were identified by filtering the RNA-Seq data with the following cutoff criteria: a twofold change in expression level and p < 0.05. Gene enrichment terms from the Gene Ontology (GO) analysis were obtained using DAVID. Pathway analysis was performed using GeneMANIA. […]

Pipeline specifications

Software tools FANSe, FANSe2, DESeq, GeneMANIA
Application RNA-seq analysis
Organisms Homo sapiens, Mus musculus
Diseases Neoplasms