title: Illumina HiSeq 2500 sequencing; RNA sequencing of Mus musculus T helper cell type 2 with retroviral overexpression of different genes
design: RNA sequencing of Mus musculus T helper cell type 2 with retroviral overexpression of different genes
library_construction_protocol: T helper type 2  cells were extracted from mouse spleens and activated with CD3/CD28. Each mouse replicate is a separate purification of T cells from a collection of mice. Mice were 8-12 weeks old and of mixed gender.  Cells were spinoculated with retroviruses overexpressing a gene of interest on day 1. IL4 is 10ng/ml, and the cells were in treated with this for the remainder of the time spent in culture. For the overexpression for chipseq and rnaseq you can refer to Addgene plasmids #117263-117267. On day 4, BFP-positive (infected) cells were FACS sorted and measured by a variant of SMART-seq2. Further information can be found in the preprint here: https://www.biorxiv.org/content/early/2017/12/28/196022 or E-MTAB-6285. Lrrc40dec is a truncated version of Lrrc40.  Cells were lysed with RLT+ and RNA purified using ampure XP beads A modified version of SMARTseq2