N_THY_RNA Biological Replicate 2
Human papillary thyroid carcinoma cell lines containing the BRAF V600E mutation, MDA-T32, MDA-T41 and thyroid origin cell line N-thy-ori-3-1 were procured from ATCC. All the cell lines were grown in RPMI-1640 (R8758, Sigma) containing 10% fetal calf serum (11550356, Gibco), glutamine (G7513, Sigma), and ampicillin/streptomycin (P4333, Sigma) in an incubator (Galaxy 170R, Eppendorf) having 5% CO 2 at 37C. The cell lines were routinely tested for mycoplasma contamination using a kit (Sigma, MP0035).Trizol method was used for extraction. NEB next ultra II RNA library preparation (E7770L catalog ID). Paired end libraries were generated and sequenced on 2*150Bp. Reads were quantified against GenCode Human reference version 37 using Salmon 1.4.0 with auto-library type detection; position, sequence and GC bias correction; and using 100 bootstraps tximport 1.22.0 under R 4.0.3 was used to summarize Gene-level counts from Transcript-levels using length-Scaled TPMPrefiltering was performed to remove Genes with less than 10 reads across the samples before performing differential expression using DESeq2 1.30.1 under R 4.0.3Gencode Version 37 for Human was used to quantifyZip files containing salmon quantification for 6 samples with bootstrap values of the inferential replicates