RA-2
Homo sapiens
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).
ENA-FIRST-PUBLIC
2019-03-31T17:01:52Z
ENA-LAST-UPDATE
2018-04-04T21:37:17Z
External Id
SAMEA1057891
INSDC center name
GSK (GlaxoSmithKline)
INSDC first public
2019-03-31T17:01:52Z
INSDC last update
2018-04-04T21:37:17Z
INSDC status
public
Submitter Id
E-MTAB-6638:RA-2
broker name
ArrayExpress
common name
human
disease
rheumatoid arthritis
individual
P1342083
institute
T17
medication
NSAID and CDMARD
organism part
synovial membrane
sample name
E-MTAB-6638:RA-2
sampling site
knee
scientific_name
Homo sapiens
sex
female
swelling
low
swollen joint count
1