title: GSM6586701: COLD24-2_R1_L002; Mus musculus; RNA-Seq
library_construction_protocol: RNA was purified from liver using RNeasy mini kit was used (Qiagen, 74106). Samples were submitted to the University of Wisconsin-Madison Biotechnology Center for RNA sequencing. Briefly, RNA size and purity were verified using Qubit<https://products.invitrogen.com/ivgn/product/Q32851?ICID=search-product> RNA HS Assay Kit  (Invitrogen, Carlsbad, California, USA) and Agilent RNA HS chip (Agilent Technologies, Inc., Santa Clara, CA, USA), respectively. Samples were prepared according the TruSeq  Stranded mRNA Library Prep kit (Illumina Inc., San Diego, California, USA) with minor modifications. Libraries were purified using AMPure XP beads (Beckman Coulter, A63880) and sequenced on the NovaSeq 2x150 bp with 30 million reads per sample. Reads were trimmed using trimming software skewer (Jiang et al.2014), filtered for at or near zero expression, and gene expression normalization was carried out by the method of trimmed mean of M-values (TMM). The trimmed single- or paired-end reads are aligned against the selected reference genome sequence using STAR (Spliced Transcripts Alignment to a Reference) (Dobin et al. 2013). Analysis of differentially expressed genes is performed with a glm using the edgeR package (Robinson, McCarthy, and Smyth 2010).