GSM4059312: 2_PEG_FRC_N503_N702 PEG FRC 36.1 36 1.6 1.31144937859286; Mus musculus; RNA-Seq
For each mouse, 1,000 PP FRCs or HEV ECs were sorted into 5 ml/well of TCL (Qiagen #1031576) buffer containing 1% 2-mercaptoethanol. RNA was isolated using RNAClean XP beads (Agencourt A63987). Template switching, cDNA synthesis and cDNA amplification were adapted from previous studies41. Libraries were prepared using the Nextera kit (Illumina).  Libraries were sequenced using an Illumina HiSeq yielding, on average, 27.5 million reads pairs per sample. RNA-sequencing data were analyzed using HTSeqGenie package in BioConductor42 as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or rRNA and adapter contamination were removed. The reads that passed were then aligned to the reference genome GRCh37 using GSNAP43. 1.6 - 4.3 % reads were of low quality and were removed. The percentage rRNA contamination ranged from 1.16 - 4.64 %. These were also removed. Reads that were uniquely mapped were used for subsequent analysis.
GEO Accession
GSM4059312