title: Illumina HiSeq 2500 paired end sequencing; RNA-seq of human tissues
design: RNA-seq of human tissues
library_construction_protocol: Sample preparation Human tissue samples used for protein and mRNA expression analyses were collected and handled in accordance with Swedish laws and regulation and obtained from the Department of Pathology, Uppsala University Hospital, Uppsala, Sweden as part of the sample collection governed by the Uppsala Biobank (http://www.uppsalabiobank.uu.se/en/). All human tissue samples used in the present study were anonymized in accordance with approval and advisory report from the Uppsala Ethical Review Board (Reference # 2002 - 577, 2005 - 338 and 2007 - 159 (protein) and  # 2011 - 473 (RNA)) Tissue samples were embedded in Optimal Cutting Temperature (O.C.T.) compound and stored at – 80°C. A n HE stained frozen section (4 μm) was prepared from each sample using a cryostat and the CryoJane® Tape - Transfer System (Instrumedics, St. Louis, MO, USA). Each slide was S 2 examined by a pathologist to ensure sampling of representative normal tissue. Three sections (10 μm) were cut from each frozen tissue block and collected into a tube for subsequent RNA extraction. The tissue was homogenized mechanically using a 3 mm steel grinding ball (VWR). Total RNA was extracted from cell lines and tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manuf acturer’s instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio - Rad Laboratories, Hercules, CA, USA) with the standard - sensitivity RNA chip or an Agilent 2100 Bioanalyzer system (Agilent Biotec hnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Only samples of high - quality RNA (RNA Integrity Number ≥7.5) were used in the following mRNA sample preparation for sequencing. Strand-specific RNA-seq (Illumina TruSeq Stranded mRNA HT kit with polyA-selection)
attributes.tag: Experimental Factor: organism part
attributes.value: liver