title: RNAseq of FACS sorted sLN_Pdgfra_pos
design: Paired-end  RNA-seq libraries were constructed from 747 pg of RNA using the SMARTer + NexteraXT Low Input RNA Kit. Libraries were then sequenced on an Illumina HiSeq yielding, on average, 35 million read pairs (2x50bp) per sample. We used salmon version 0.6 (Patro R, Duggal G, Kingsford C. Accurate, fast, and model-aware transcript expression quantification with Salmon. bioRxiv 2015) to quantitate reads against the the GENCODE M9 mouse transcript models with "--biasCorrect"  enabled and the "-l IU" library type. These data were imported into R using the tximport package (Soneson C, Love MI and Robinson MD. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research 2016) to get gene level expression estimates, and limma/voom (Law, CW, Chen, Y, Shi, W, Smyth, GK. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biology 2014) was used for differential expression analysis.