Distinct cellular and spatial niches within the inflamed synovium of childhood arthritis [scRNA-Seq]
Single-cell RNA-seq · human · 46 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 46 samples: 46 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
- Synovial tissue atlas in juvenile idiopathic arthritis reveals pathogenic niches associated with disease severityScience translational medicine · 2025
Read the full summary ↓
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 GSE278962_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1169842 and SRA study SRP537199. 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 46 sample titles: 46 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.
- GSM8558909 2519_01_Blood_total RNA
- GSM8558910 2519_01_Synovial Fluid_total RNA
- GSM8558911 2519_01_Blood_protein
- GSM8558912 2519_01_Synovial Fluid_protein
- GSM8558913 2519_04_Blood_total RNA
- GSM8558914 2519_04_Synovial Fluid_total RNA
- GSM8558915 2519_04_Blood_protein
- GSM8558916 2519_04_Synovial Fluid_protein
- GSM8558917 2519_05_Blood_total RNA
- GSM8558918 2519_05_Synovial Fluid_total RNA
- GSM8558919 2519_05_Blood_protein
- GSM8558920 2519_05_Synovial Fluid_protein
- GSM8558921 2518_11_Tissue_total RNA
- GSM8558922 2518_11_Blood_total RNA
- GSM8558923 2518_11_Synovial Fluid_total RNA
- GSM8558924 2518_11_Blood_protein
- GSM8558925 2518_11_Synovial Fluid_protein
- GSM8558926 2518_8_Tissue_total RNA
- GSM8558927 2518_8_Blood_total RNA
- GSM8558928 2518_8_Synovial Fluid_total RNA
- GSM8558929 2518_8_Blood_protein
- GSM8558930 2518_8_Synovial Fluid_protein
- GSM8558931 2519_5_Tissue_total RNA
- GSM8558932 2518_4_Tissue_total RNA
- GSM8558933 2519_7_Blood_total RNA
- GSM8558934 2519_7_Synovial Fluid_total RNA
- GSM8558935 2519_7_Blood_protein
- GSM8558936 2519_7_Synovial Fluid_protein
- GSM8558937 2519_08_Tissue_total RNA
- GSM8558938 2519_08_Blood_total RNA
- GSM8558939 2519_08_Synovial Fluid_total RNA
- GSM8558940 2519_08_Blood_protein
- GSM8558941 2519_08_Synovial Fluid_protein
- GSM8558942 2518_14_Blood_total RNA
- GSM8558943 2518_14_Blood_protein
- GSM8558944 2518_14_Synovial Fluid_total RNA
- GSM8558945 2518_14_Synovial Fluid_protein
- GSM8558946 2518_14_Synovial Tissue_total RNA
- GSM8558947 2518_17_Blood_total RNA
- GSM8558948 2518_17_Blood_protein
+ 6 more — browse all 46 samples with per-sample file links →
- GSE294277 Integrative single cell RNA-sequencing and spatial transcriptomics uncovers distinct macrophage-fibroblast cross-talk in human hip synovium between patients with femoroacetabular impingement and osteoarthritis 22 samples shares arthritis, distinct, synovium, spatial
- GSE278688 Integrated Single-Cell and Spatial Transcriptomics Uncover Distinct Cellular Subtypes Involved in Neural Invasion in PDAC [scRNA-Seq] 29 samples shares scrna-seq, distinct, cellular, spatial
- GSE278694 Integrated Single-Cell and Spatial Transcriptomics Uncover Distinct Cellular Subtypes Involved in Neural Invasion in PDAC 88 samples shares distinct, cellular, spatial
- GSE272347 Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [scRNA-seq] 17 samples shares scrna-seq, cellular
- GSE270680 A spatially resolved atlas of gastric cancer characterises a lymphocyte aggregated region [scRNA-seq] 77 samples shares scrna-seq, spatial
- GSE190564 Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - whole tissue scRNA-Seq 62 samples shares scrna-seq, spatial
- GSE283079 Bulk RNA-seq of human knee osteoarthritis synovium 41 samples shares arthritis, synovium
- GSE246215 Cross-tissue human fibroblast atlas reveals myofibroblast subtypes with distinct roles in immune modulation [scRNA-seq] 38 samples shares scrna-seq, distinct
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.