GSM1973550: Tvd-ID133079-A; Mus musculus; RNA-Seq
Total RNA from liver or tumor tissue was purified as described elsewhere (5). Briefly, tissue was homogenized in Trizol (Invitrogen) and chloroform was added. After centrifugation, RNA was purified using RNeasy Mini columns (Qiagen) according to the manufacturers protocol, including the on-column DNase I digestion step. 1µg total RNA was retro-transcribed into cDNA using the reverse transcriptase ImPromII (Promega) and oligodT and random primers. 10ng of cDNA were used for each quantitative reverse transcriptase PCR (qRT-PCR) analysis. Amplification was performed with the FAST SYBR Green Master Mix and quantified using the 7500 Fast Real-Time PCR machine (both Applied Biosystems).   For RNA sequencing, 5µg of total RNA of good quality (RNA integrity number ≥ 7.5) were treated according to the Ribozero rRNA removal kit (Epicentre) and purified on RNeasy MinElute columns (Qiagen). RNA integrity and successful removal of ribosomal RNA were assessed with the Agilent 2100 Bioanalyser (Agilent Technologies) or the LabChip® GX II Gel Electrophoresis (PerkinElmer). RNA-seq libraries were prepared with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s protocol starting from the RNA fragmentation step.