title: GSM3446077: SOD1; Mus musculus; RNA-Seq
library_construction_protocol: “TruSeq Stranded mRNA Sample Prep kit” (Illumina, San Diego, CA) was used for library preparation. Libraries were processed with Illumina cBot for cluster generation on the flow cell and sequenced on single-end mode at the multiplexing level requested on HiSeq. 2500 (Illumina, San Diego, CA). The Illumina pipeline based on CASAVA version 1.8.2 of the was used to process raw data for both format conversion and de-multiplexing. Standard bioinformatics analysis was provided by the IGA facility. Briefly, the reads produced (on average 56.4 M reads/sample; min 47.6 M, max 76.8 M) were first put through the sequencing pipeline made of base-calling on the Illumina Pipeline, trimming (min length 35) with ERNE and removal of adapter sequences with Cutadapt. Reads were then aligned to GRCm38 reference genome/transcriptome using TopHat. Overall alignment rate was 95% for all the samples. Cuffdiff was used to perform differential expression analysis Libraries were processed with Illumina cBot for cluster generation on the flow cell and sequenced on single-end mode at the multiplexing level requested on HiSeq. 2500 (Illumina, San Diego, CA).
attributes.tag: GEO Accession
attributes.value: GSM3446077