title: GSM5700280: 8_HSV-2pos_dLN; Mus musculus; RNA-Seq
library_construction_protocol: cells were sorted into SMART-seq v4 Ultra Low Input (Takara Bio USA, San Jose, California) lysis buffer and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries.  Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies). Dual-index, single-read sequencing of the pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.  FASTQs were aligned to a mouse reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count.  QC and metrics analysis was performed using the Picard family of tools