RNA-Seq analysis of human colorectal cancer with liver metastasis. Homo sapiens

Nine specimens from three colorectal cancer (CRC) patients including adjacent normal tissue, primary tumor, and lever metastasis tissue, and three specimens from 3 CRC patients without liver metastasis were collected for RNA sequencing analysis. Overall design: Nine specimens from three colorectal cancer (CRC) patients including adjacent normal tissue, primary tumor, and lever metastasis tissue, and three specimens from 3 CRC patients without liver metastasis were collected for RNA sequencing analysis. The mRNA libraries were separately generated from total RNA and constructed according to the standard Illumina mRNA library preparation (Illumina Inc, USA). Sequencing was done on the Illumina Nextseq 500 platform according to the manufacturer’s instructions. Images generated by Nextseq 500 were converted into nucleotide sequences by a base calling pipeline and stored in FASTQ format and the dirty raw reads were filtered out prior to analyzing the data. Clean reads were mapped to reference Homo sapiens transcriptome sequences from the UCSC website (hg19) using Bowtie2 and Tophat 2.0.1 software. To annotate gene expression, reads per kilo bases per million reads (RPKM) values of each gene were calculated, and differentially expressed genes (DEGs) were extracted using this value.