title: Illumina HiSeq 2500 paired end sequencing; Integration of miRNA:mRNA co-expression revealed crucial mechanisms modulated in immunogenic cancer cell death
design: Integration of miRNA:mRNA co-expression revealed crucial mechanisms modulated in immunogenic cancer cell death
library_construction_protocol: Mino (human mantle cell lymphoma, ATCC CRL-3000) cell lines were cultured in RPMI 1640 (Sigma, now Merck), while MDA-MD-231 cell line (human breast adenocarcinoma, ATCC HTB-26) was cultured in DMEM (Sigma, now Merck); both media were supplemented with 10% FCS (Fetal Calf Serum, Gibco) and 100 µg/mL streptomycin, and 100 IU/mL penicillin (Sigma, now Merk) and maintained at 37°C in a humidified 5% CO2 atmosphere. Cell death was induced with human IFN-a (IntronA SP Europe) and 9-cis-Retinoic Acid (Sigma, now Merck) used at 1000 U/ml and 1 µmol/L, respectively, for 48 h, or Doxorubicin (Sigma, now Merck) used at 0.5 µM, for 24 h. As control tumor cells were irradiated with 80 gray for 16 minutes Cell death was induced with human IFN-a (IntronA SP Europe) and 9-cis-Retinoic Acid (Sigma, now Merck) used at 1000 U/ml and 1 µmol/L, respectively, for 48 h, or Dox-orubicin (Sigma, now Merck) used at 0.5 µM, for 24 h. As control tumor cells were irradi-ated with 80 gray for 16 minutes Total RNA was extracted as described previously in Tarallo et al. (Tarallo et al., 2016 Genome Biology) Indexed libraries were prepared from 1 µg/ea. purified RNA with Tru- Seq Stranded Total RNA Sample Prep Kit (Illumina Inc.) according to the manufacturers instructions. Li-braries were sequenced (paired-end, 2 x 100 cycles) at a concentration of 8 pmol/L per lane on HiSeq2500 platform (Illumina Inc.).