RNA-seq of thyroid cancer cell line upon silencing of RAIN, a RUNX2 associated intergenic lncRNA, and RUNX2
Cells were collected after 10 days from selection. TPC1 cells were cultured in DMEM medium supplemented with 10% FBS and 1% P/S. MDA-T41 cells were grown in RPMI-1640 supplemented with 1% non-essential amino acids, 10% FBS and 1% penicillin-streptomycin. All cell lines were grown at 37°C/ 5% CO2 and routinely tested for mycoplasma infection. Cells were infected with pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-Puro containing either sgRAIN, sgRUNX2 or sgNT, then selected with 1 µg/ml Puromycin for 3 days. Total RNA was extracted by Maxwell RSC simplyRNA Cells kit (Promega, Madison, Wisconsin, USA) Libraries were obtained starting from 100ng of total RNA following the Illumina Stranded Total RNA preparation Ligation with Ribo-Zero Plus protocol.