title: GSM6133932: Tumoral samples, 366; treatment: DOX; Mus musculus; RNA-Seq
library_construction_protocol: For RNAseq, total RNA was extracted using the miRVana miRNA isolation kit (ThermoFisher), following the manufacturer´s recommendations. Between 0.8 and 1 µg of total RNA was extracted from organoids after dissociating the Matrigel/BME form the cultures (as indicated above). RIN (RNA integrity number) numbers were always in the range of 9 to 10 (Agilent 2100 Bioanalyzer). 250ng of total RNA samples were used. Average sample RNA Integrity Number was 9.1 (range 8.2-9.8) when assayed on an Agilent 2100 Bioanalyzer. Sequencing libraries were prepared with the "QuantSeq 3' mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. [This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation]. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries were completed by PCR, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq 2500 with v4 Chemistry by following manufacturer's protocols. QuantSeq 3' mRNA-Seq