Computational protocol: A Critical Role for IL-17RB Signaling in HTLV-1 Tax-Induced NF-κB Activation and T-Cell Transformation

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Protocol publication

[…] Total RNA was prepared from parental primary T cells, HTLV-1-infected cells after 1 week of co-culture, HTLV-1 immortalized T cell clones after 12 weeks of co-culture or MT-2 cells. Dead cells were removed from co-cultured cells after magnetic labeling and separation using the Dead Cell Removal Kit (Miltenyi Biotec). RNA was isolated with RNeasy columns (Qiagen). RNA-Seq and bioinformatics were conducted by the Johns Hopkins Sidney Kimmel Cancer Center next-generation sequencing core. Sequencing analysis was performed by aligning the paired end reads to hg19 using Bioscope. The differential expression analysis was performed using the DEseq R package and the GO enrichment was done with the topGO R package. […]

Pipeline specifications

Software tools DESeq, TopGO
Application RNA-seq analysis
Organisms Human T-cell leukemia virus type I, Homo sapiens
Diseases Spinal Cord Diseases, Leukemia, T-Cell, Leukemia-Lymphoma, Adult T-Cell, Paraparesis, Tropical Spastic, Lymphoma, T-Cell