Loss of synovial tissue macrophage homeostasis precedes Rheumatoid Arthritis clinical onset
RNA-seq (gene expression) · human · 26 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 26 samples: 26 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Loss of synovial tissue macrophage homeostasis precedes rheumatoid arthritis clinical onsetScience advances · 2024
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE246421_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1032911 and SRA study SRP468820. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 26 sample titles: 26 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM7868613 RA1 BXN ++
- GSM7868614 RA1 BXN --
- GSM7868615 RA2 BXN ++
- GSM7868616 RA2 BXN --
- GSM7868617 RA4 BXN ++
- GSM7868618 RA4 BXN --
- GSM7868619 RA5 BXN ++
- GSM7868620 RA5 BXN --
- GSM7868621 RA6 BXN ++
- GSM7868622 RA6 BXN --
- GSM7868623 RA7 BXN ++
- GSM7868624 RA7 BXN--
- GSM7868625 RA8 BXN ++
- GSM7868626 RA8 BXN --
- GSM7868627 RA9 BXN ++
- GSM7868628 RA9 BXN --
- GSM7868629 RA10 BXN ++
- GSM7868630 RA10 BXN --
- GSM7868631 RA3 SFMC ++
- GSM7868632 RA3 SFMC --
- GSM7868633 RA10 SFMC ++
- GSM7868634 RA10 SFMC --
- GSM7868635 RA12 SFMC ++
- GSM7868636 RA12 SFMC --
- GSM7868637 RA14 SFMC ++
- GSM7868638 RA14 SFMC --
- GSE314080 Transcriptional Profiling of Synovial Macrophages using Minimally Invasive Ultrasound-Guided Synovial Biopsies in Rheumatoid Arthritis [dataset2] 24 samples shares macrophage, rheumatoid, arthritis, synovial
- GSE296117 A single-cell RNA-seq dataset of synovial fluid from rheumatoid arthritis treated with TNF-α/JAK inhibitor 18 samples shares rheumatoid, arthritis, synovial
- GSE279915 Complexity of synovial fluid-derived monocyte–macrophage lineage cells in knee osteoarthritis 12 samples shares macrophage, arthritis, synovial
- GSE342939 Senescent activated naive B cells promote anti-citrullinated antigen T cell responses and the transition to clinical rheumatoid arthritis 78 samples shares rheumatoid, arthritis, clinical
- GSE274680 Inflammation and lymphocyte activation during longitudinal progression to rheumatoid arthritis in at-risk individuals 243 samples shares rheumatoid, arthritis
- GSE292338 RNAseq analysis of human neutrophils from healthy controls, people with frailty and people with rheumatoid arthritis 39 samples shares rheumatoid, arthritis
- GSE250242 Single cell RNA and TCR sequencing reveals substantive similarities between synovial fluid and synovial tissue T-cells in inflammatory arthritis. 21 samples shares arthritis, synovial
- GSE307297 Single cell RNAseq on rheumatoid arthritis-related interstitial lung disease 12 samples shares rheumatoid, arthritis
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.