Rnase easy plus mini kit

To measure the effect of hypoxia on gene expression patterns, we used RNAseq technology as part of a larger project that has been deposited in NCBI’s Gene Expression Omnibus (29) and are accessible through GEO Series accession number GSE125511 (https://www.ncbi.nih.gov/geo/query/acc.cgi?acc=GSE125511). Briefly, RNA (RIN >9) was extracted from UFH-001 cells, previously exposed to normoxia or hypoxia for 16h in the presence or absence of BCP at either 20 μM or 200 μM (RNase easy plus mini kit from Qiagen). Libraries were prepared at the Genomics Core at the University of Louisville and sequencing was performed on triplicate biological replicates (Illunima NestSeq 500), generating over 144 million 75 bp reads that aligned to the human genome (96.3% alignment rate), or approximately 24 million reads per sample. The RNAseq data were analyzed using the tuxedo suite pipeline (fastqc, trimmomatic, tophat2, cufflinks, and cuffnorm) by the KBRIN Bioinformatics Core. Differential gene expression between hypoxia and normoxia was determined with cuffdiff with a q-value cutoff ≤ 0.05.