2025-06-06
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA115131451
External Id
Centre for Experimental Medicine & Rheumatology, Queen Mary University of London
INSDC center name
2024-01-24T12:04:51Z
INSDC last update
public
INSDC status
ERS17835732
SRA accession
E-MTAB-13733:Sample 160
Submitter Id
0
acr20_response
56
year
age
46
arthritis.activity
ArrayExpress
broker name
positive
ccp_status
Bpoor
cell.type (bcell)
not collected
collection date
human
common name
5
milligram per liter
crp
Protocols: Patients underwent a synovial biopsy of a clinically active joint (clinically swollen and with ultrasound synovial thickening ≥2) before starting trial therapy. For the full study protocol and baseline patient characteristics see Rivellese et al., 2023 https://www.thelancet.com/journals/lanrhe/article/PIIS2665-9913(23)00241-2/fulltext Image analysis and base calling were conducted by the NovaSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de- multiplexed using Illumina's bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification. A minimum of 6 synovial samples per patient were immediately immersed in RNA-Later and RNA was extracted from synovial tissue using Qiagen Micro AllPrep RNA/DNA extraction kit. Briefly, 1-10mg of tissue was lysed using RLT buffer with addition of β-Mercaptoethanol, and then sheared using Qiagen TissueLyser II machine.Tissue lysate was then run through the kit columns set. Columns were washed using the appropriate kit wash buffers before RNA was eluted and re-suspended in RNAse free water. For more details see: https://www.thelancet.com/cms/10.1016/S2665-9913(23)00241-2/attachment/94785fe7-25eb-4792-8ea3-501537b9c5bc/mmc1.pdf RNA sequencing library preparation used the NEBNext Ultra II RNA Library Prep Kit for Illumina followed by manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNA were first enriched with Oligod(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 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA).
description
established RA
developmental stage
rheumatoid arthritis
disease
21
millimeter
esr
Any other mixed backgound
ethnicity
not collected
geographic location (country and/or sea)
STRAPPAT00182
individual
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
synovial tissue
organism part
Myeloid
pathotype
30
physicians.global.assessment
positive
rf_status
STRAPPAT00182-baseline
sampleid
Homo sapiens
scientific_name
female
sex
6
count unit
swollen_joints_counts_sjc
9
count unit
tender_joints_counts_tjc
Sample 160
title
2
week
visit