Computational protocol: Intact CD100–CD72 Interaction Necessary for TCR-Induced T Cell Proliferation

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Protocol publication

[…] RNA samples were prepared using SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech). Libraries were clustered using cBot and sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 2 × 126 setup in Rapid High Output mode. Sequence reads were mapped to reference transcriptome TopHat. Gene level abundance was estimated by HTSeq and batch effects were removed by DESeq. […]

Pipeline specifications

Software tools HSC, TopHat, HTSeq, DESeq
Application RNA-seq analysis
Diseases Neoplasms