Protocols: A minimum of 6 samples (ultrasound-guided synovial biopsies) per patient were immediately immersed in RNA-Later. All patients provided written informed consent before the synovial tissue biopsy procedure. They were fulfilling 2010 ACR/EULAR classification criteria for RA and were eligible for treatment with rituximab therapy according to UK NICE guidelines, i.e. failing or intolerant to csDMARD therapy and at least one biologic therapy (excluding trial IMPs) were recruited when fulfilling the trial inclusion/exclusion criteria (for the full study protocol and baseline patient characteristics see Humby et al). The patients were recruited under R4RA clinical trial. For the full study protocol and baseline patient characteristics see Humby et al., 2021 https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32341-2/fulltext#fig1 Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification. Tissue was lysed in Trizol solution using a LabGen125 homogeniser. Then samples were extracted using Zymo Direct-zol Miniprep kits as per the manufacturer's instructions. Briefly, 1-10mg of tissue lysate was run through the Zymo-Spin IC Column. Columns were then washed using the appropriate kit wash buffers before RNA was eluted and re-suspended in RNAse free water. Quality control was carried out by quantifying samples by spectrophotometer readings on a Nanodrop ND2000C. RNA integrity was measured using Pico-chip technology on an Agilent 2100 Bioanalyzer to determine a RIN (RNA integrity number). RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligo d(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3'ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
ENA first public
2022-04-16
ENA last update
2022-04-16
External Id
SAMEA13989240
INSDC center alias
Centre for Experimental Medicine & Rheumatology, Queen Mary University of London
INSDC center name
Centre for Experimental Medicine & Rheumatology, Queen Mary University of London
INSDC first public
2022-04-16T00:27:41Z
INSDC last update
2022-04-16T00:27:41Z
INSDC status
public
Submitter Id
E-MTAB-11611:Sample 157
age
63
anti-cyclic citrullinated peptide antibody measurement
positive
arthritis disease activity score measurement
62
broker name
ArrayExpress
cdai.response.status.v7
Responder
cell.type (bcell)
Brich
clinical history
difficult to treat rheumatoid arthritis
common name
human
crp
10
disease
rheumatoid arthritis
esr
69
ethnic group
Caucasian
imputed.logcrp1
Raw
imputed.logesr
Raw
imputed.pga
Raw
imputed.sjsqrt
Raw
imputed.tjsqrt
Raw
imputed.vas
Raw
individual
R4RAPAT00135
organism part
synovial tissue
pathotype
Lymphoid
physicians.global.assessment
50
rheumatoid factor measurement
negative
sample id
R4RAPAT00135-week0
sample name
E-MTAB-11611:Sample 157
sex
female
swollen_joints_counts_sjc
4
tender_joints_counts_tjc
18
visit
0