characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2019-03-31T17:01:52Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-04-04T21:37:17Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA1057895
characteristics.characteristic: External Id
characteristics.text: GSK (GlaxoSmithKline)
characteristics.characteristic: INSDC center name
characteristics.text: 2019-03-31T17:01:52Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-04-04T21:37:17Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS2363483
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-6638:RA-6
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: All donors provided written informed consent for use of their material, and the collection and use of the samples received Institutional Review Board review and approval. Of the seventeen synovial biopsy samples progressed for RNA-Seq and DNA methylation analyses, fifteen were obtained from knee and two from ankle. Samples were collected from 6 male and 11 female patients and under different medication regimens: no medication, non-steroid anti-inflammatory drugs (NSAID), conventional and biological disease-modifying anti-rheumatic drugs (CDMARD and BDMARD), and combinations thereof. All patients underwent arthroscopic synovial tissue biopsy sampling of an actively inflamed knee joint or ankle. Samples were flash frozen upon collection. Synovial biopsies were disrupted and homogenised in Buffer RLT Plus and β-mercaptoethanol (β-ME) using QIAshredder spin columns followed by simultaneous isolation of DNA and Total RNA using a AllPrep DNA/RNA Mini kit (Qiagen). RNA samples were quantified and their integrity assessed using Qubit RNA Broad Range Assay Kit (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies) respectively. Depending on sample yield, DNA samples were quantified using Qubit DNA BR or Qubit DNA HS kit (Thermo Fisher Scientific). 100ng of sample DNA was used in the bisulfite conversion procedure. Bisulfite conversion was performed using the EZ DNA Methylation-Lightning Kit (Zymo Research). Each bisulfite conversion reaction contained 500pg of unmethylated lambda DNA (Promega) as an internal control. This was used as control to verify bisulphite conversions efficiencies were at least 98%. Methyl-Seq libraries were prepared using an EpiGnome Methyl-Seq Library Preparation Kit (Epicentre, now Illumina). Two rounds of qPCR quantification of the final libraries were performed with the KAPA Library Quantification Kit (KAPA Biosystems) on a 7900HT Real-Time PCR System (Thermo Fisher Scientific).
characteristics.characteristic: description
characteristics.text: rheumatoid arthritis
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000685
characteristics.characteristic: disease
characteristics.text: P4539483
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0011020
characteristics.characteristic: individual
characteristics.text: T35
characteristics.characteristic: institute
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: synovial membrane
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/FMA_66762
characteristics.characteristic: organism part
characteristics.text: knee
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0001465
characteristics.characteristic: sampling site
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000384
characteristics.characteristic: sex
characteristics.text: high
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/EO_0007075
characteristics.characteristic: swelling
characteristics.text: 11
characteristics.characteristic: swollen joint count
characteristics.text: RA-6
characteristics.characteristic: title