GSM3259903: CON_477_SAL_M_ACTTGA; Mus musculus; RNA-Seq
Bilateral striatal tissue was homogenized with an RNase-free disposable pellet pestle (Thermo Fisher Scientific, Waltham, MA) and RNA was extracted using the commercially available RNeasy® Lipid Tissue Mini Kit (Qiagen Inc., Valencia, CA). Purification of the isolated RNA included treatment with DNase I (Qiagen Inc, Valencia, CA), accordingly to the manufacturer's instructions. For assessing total RNA yield, aliquot samples were measured with the Qubit® 2.0 (Life Technologies). Each sample showed a 260/280 ratio over 2.0 and yielded over 14 μg of RNA. Quality and integrity of isolated RNA samples were determined by 28S/18S rRNA analysis with the Agilent 2100 Bioanalyzer (Santa Clara, CA). All samples scored an RNA Integrity Number (RIN) over 8, indicating no signs of degradation. Quality was spot checked by choosing random samples to run on a gel, which confirmed the Bioanalyzer report. RNA-sequencing was performed by the Roy J. Carver Biotechnology Center. RNA-Seq libraries were prepared using the TruSeq Stranded RNA Sample Prep kit with an average fragment length of 200 bp. Libraries were quantified using qPCR, pooled in a pool of 20, and multiplexed across a total of 5 lanes. The libraries were sequenced on an Illumina HiSeq 2500 for 101 cycles in 100 bp paired-end format using a TruSeq SBS sequencing reagent kit, v. 4. Read depth ranged between 41,684,484 reads and 70,449,689 reads with a median read depth of 54,516,050 reads.