RNA-seq Analysis of Human Genome

The total RNAs were isolated and used for high-throughput sequencing with TruSeq v3 chemistry (San Diego, CA 92121, USA) and 50 bp single reads on an Illumina HiSeq 2000. For RNA-seq analysis, sequenced reads were aligned to the Homo sapiens genome (version GRCh38.p8 from NCBI) using TopHat 2.1.1 [27 (link)] linked to Bowtie 2.2.8 [28 (link)] with the default sensitive settings. From the sequenced reads, transcripts were assembled using Cufflinks 2.2.1 [29 (link)]. Differential expression analyses were performed with Cuffdiff 2.2.1 [30 (link)] using a minimum false-discovery rate (qvalue) of <0.002 as statistical significance and log2 fold change >1.5 as the cut-off. Additional information for each gene was obtained from the NCBI database and included in the dataset. Genes with expression levels under a threshold in both the control and treatment conditions were discarded. The median of the distribution of the non-zero values was taken as the threshold. The generated data were uploaded to the FIESTA viewer FIESTA@BioinfoGP (https://bioinfogp.cnb.csic.es/tools/FIESTA/index.php)