Time series RNA-seq of Na?ve CD4 positive T-cells undergoing differentiation towards T-helper 1.

In eukaryotes, mRNA abundance is often a poor proxy for protein abundance. Despite this, the majority of methods used to dissect function in mammalian biology involve measurements of mRNA, with the assumption that changes observed at the mRNA level are reflected at the protein level. The inability to predict protein abundance from mRNA abundance is a major limitation when dissecting the relationship between genotype and phenotype in mammals. To understand the effect of cell-type, splice-variant selection and translation rate on the relationship between mRNA and protein abundance, we performed RNA-sequencing and mass-spectrometry proteomics of primary human na?ve CD4+ T helper (NTH) cells at six time points during differentiation into T-helper type 1 (TH1) cells. For the RNA- sequencing, NTH cells were isolated from Human blood donors, subjected to T-helper 1 stimulation (anti-CD3/CD28, IL2 and IL12) for 0.5, 1, 2, 6 and 24 hours. At each time point cells were harvested, snap frozen and stored at -80 degrees Celsius. RNA was isolated from each sample and sequenced on an illumina 2500 instrument. By combining the information from the RNA- sequencing and the proteomics we constructed a simple mRNA-protein model, in which protein expression was defined as a linear combination of the splice variants of a gene, with a time-delay accounting for the dynamical effect induced by post-transcriptional processes and protein synthesis. This simple dynamical model resulted in a gene-protein correlation of rhoTH1 = 0.86, significantly higher than previously reported gene-protein prediction models in mammals.