Illumina HiSeq 2500 sequencing; RNA-seq of human hepatocellular carcinoma (HCC) patients
RNA-seq of human hepatocellular carcinoma (HCC) patients
Tissue specimens were obtained from patients undergoing liver resection of HCC from the Australian Victorian Biobank, according to the approval of local ethics committee [application number: 2010/541-31/1; 2017/719-31/2]. Material was fresh frozen and stored at -80 Celsius degrees at the facilities of the Australian Victorian Biobank and shipped to Karolinska Institutet on dry ice. Total RNA was extracted from liver biopsies using the RNeasy mini kit (Qiagen) and treated with DNase RNAase free kit (Qiagen). RNA extraction 1. Excise 10 mg liver tissue sample (on dry ice) into 1.5 ml Eppendorf tubes. 2. Remove the sample tube from the dry ice and immediately pipet 600 ul of  RLT lysis buffer + b-mercaptoethanol into each sample tube. 3. Homogenize immediately on the Bullet Blender tissue homogenizer 2x 3 mins, strength 8. 4. Transfer the homogenate to the Allprep column and continue with the extraction procedure following the manufacturerÂ´s instructions (RNeasy mini kit, DNase RNAase free kit (Qiagen)). Elution 2x in 50 ul of nuclease-free water. The isolated RNA was measured with a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher), and RNA concentration and integrity were assessed on an Agilent RNA 6000 Pico chip using the Agilent 2100 BioAnalyzer (Agilent Technologies).  RNA library preparation was performed using  Ribosomal depletion with the TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit at the Estonian Genome Center. The cDNA libraries were run on high-sensitivity DNA chips on the Agilent 2100 BioAnalyzer.
Experimental Factor: disease
hepatocellular carcinoma
Experimental Factor: sampling site
neoplasm