title: Illumina HiSeq 2000 paired end sequencing; An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes
design: An mRNA-sequencing atlas of mouse CD4+ T cell transcriptomes
library_construction_protocol: CD4+, CD62L+ cells were purified with CD4+CD62L+ T Cell Isolation Kit II (Miltenyi Biotec). Cells were seeded into anti-CD3 (2 ug/ml, clone 145-2C11, eBioscience) and anti-CD28 (5 ug/ml, clone 37.51, eBioscience) coated 96-well plates, at a density of 250,000-500,000 cells/ml and cultured in a total volume of 200 ul in the presence of recombinant murine IL-4 (10 ng/ml, RD Systems) and neutralizing anti-IFN-gamma (10 ug/ml, clone XMG1.2, eBioscience). Cells were cultured for another four days in absence of CD3 and CD28 stimulation to rest them. The original medium was kept and fresh medium containing the same cytokines as before was added to dilute the cultures 1:3. Finally, the cells were labelled with Propidium Iodide and FITC-conjugated antibodies against CD11b, CD11c, Ly6G, CD8a and CD19. The cultures were then FACS-sorted to obtain Propidium Iodide-, FITC-negative cells. RNA was purified using the Qiagen RNEasy Plus Mini Kit automated using a QIAcube Samples were processed using the TruSeq RNA Sample Prep v2 kit (Illumina) according to the manufacturers instructions with an alteration to use KAPA Hifi polymerase for PCR amplification instead of the one supplied with the kit.