title: GSM4142914: 3143_S7; Mus musculus; RNA-Seq
library_construction_protocol: Total RNA was homogenizated in Trizol Reagent (Sigma Aldrich). Libraries were prepared using TruSeq polyA mRNA kit (Illumina) according to manufacturer instructions, and sequenced by using the NovaSeq 6000 System (Illumina). Raw sequence reads were quality controlled through FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using Trimmomatic (v0.38) (http://www.ncbi.nlm.nih.gov/pubmed/24695404). To quantify the transcripts abundances we used Kallisto (v0.44.0) (Bray et al., 2016). Kallisto is also used to build an index from the mouse reference genome (EnsDb.Mmusculus.v79) with default parameters To import and summarize transcript-level abundance of Kallisto, Tximport an R package is used. Differential expression was assessed using DSeq2 (Love et al., 2014). Adjusted p-value less than 0.05 were selected as well as only genes > 2 fold change were considered in the analyses. RNA libraries were prepared for sequencing using standard Illumina protocols
attributes.tag: GEO Accession
attributes.value: GSM4142914