title: SH032
organism: Homo sapiens
description: Protocols: 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).
attributes.tag: ENA first public
attributes.value: 2017-12-14
attributes.tag: ENA last update
attributes.value: 2017-12-01
attributes.tag: External Id
attributes.value: SAMEA104412540
attributes.tag: INSDC center alias
attributes.value: Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
attributes.tag: INSDC center name
attributes.value: Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
attributes.tag: INSDC first public
attributes.value: 2017-12-14T17:03:09Z
attributes.tag: INSDC last update
attributes.value: 2017-12-01T13:15:16Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-6266:SH032
attributes.tag: age
attributes.value: 68
attributes.tag: body mass index
attributes.value: 30
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: human
attributes.tag: disease
attributes.value: osteoarthritis, knee
attributes.tag: organism part
attributes.value: articular cartilage of joint
attributes.tag: sample name
attributes.value: E-MTAB-6266:SH032
attributes.tag: sampling site
attributes.value: posterior lateral condyle of femur
attributes.tag: sex
attributes.value: male