GSM7437199: MCAO_3h_SH_D; Mus musculus; RNA-Seq
Samples were collected from the injured cortical region (including affected as well as non-affected brain tissue) and homogenized using the TissueLyser (QIAGEN). Total RNA was extracted with TRI Reagent (Sigma-Aldrich) according to the manufacturer's protocol and treated with TURBO DNA-free kit (Thermo Fisher). RNA quantity and purity was assessed using the NanoDrop 2000 spectrophotometer (Thermo Fisher) and RNA integrity was assessed using the Fragment Analyzer (Agilent). All samples had RQN > 8. Libraries were prepared from 400 ng total RNA with QuantSeq 30 Library Prep Kit FWD (Lexogen) according to manufacturer's protocol. 1 µl of ERCC spike-in (c = 0.01x; Thermo Fisher) per library was included. Libraries were quantified on the Qubit 2 fluorometer (Thermo Fisher) and Fragment Analyzer (Agilent), and sequenced on the NextSeq 500 high-output (Illumina) with 85 bp single-end reads. 11.5 – 38 million reads were obtained per library with a median of 16 million reads