alias: E-MTAB-6266:SH048_p
title: Illumina HiSeq 2500 paired end sequencing; RNA-Seq analysis of human osteoarthritic intact cartilage following total knee replacement
design: RNA-Seq analysis of human osteoarthritic intact cartilage following total knee replacement
library_construction_protocol: Cartilage was obtained under Ethics Committee approval with written informed consent from 60 patients with symptomatic knee osteoarthritis (OA). Cartilage from osteochondral samples were isolated from the intact PLC (posterior lateral condyle) for RNA-seq analysis. Comparable PLC samples from 10 non-OA joints were obtained from above knee amputations of patients with peripheral vascular disease and no history or clinical sign of osteoarthritis, joint disease, or joint trauma. Total RNA was extracted from each patient sample of 200 to 400 mg of cartilage using TRIzol (LifeTechnologies) reagent and homogenisation (Braun Mikrodismembrator) following freezing in liquid nitrogen. The RNA was purified using RNeasy Qiagen clean-up columns (Qiagen) and for sequencing had a RIN score of >6 (2200 TapeStation, Agilent Technologies). Strand specific RNA-seq libraries were generated from 0.5-1 ug RNA using the TruSeq Stranded mRNA assay (Illumina, Inc.) using the manufacturers Stranded mRNA Sample Preparation Kit and 101bp paired-end reads were generated. Total RNA was extracted from 200-400 mg of cartilage using TRIzol (Life-technologies) reagent and homogenisation (Braun Mikrodismembrator) following freezing in liquid nitrogen. The RNA was purified using RNeasy Qiagen clean-up columns (Qiagen) and for sequencing had a RIN score of >6 (2200 TapeStation, Agilent Technologies).
identifiers.namespace: Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
identifiers.id: E-MTAB-6266:SH048_p