Transcriptional Profiling of Synovial Macrophages using Minimally Invasive Ultrasound-Guided Synovial Biopsies in Rheumatoid Arthritis [dataset2]
RNA-seq (gene expression) · human · 24 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
- 24 samples: 15 × Sorted Macrophages from Synovial Tissue, RA, Patient vs 9 × Sorted Macrophages from Synovial Tissue, OA, PatientGroups 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
- Transcriptional Profiling of Synovial Macrophages Using Minimally Invasive Ultrasound-Guided Synovial Biopsies in Rheumatoid ArthritisArthritis & rheumatology (Hoboken, N.J.) · 2018
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 GSE314080_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 PRJNA1390053. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 2 replicated groups read from 24 sample titles; they account for 24 of them. 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.
- GSM9381245 Sorted Macrophages from Synovial Tissue, OA, Patient 6 Sorted Macrophages from…
- GSM9381246 Sorted Macrophages from Synovial Tissue, RA, Patient 14 Sorted Macrophages from…
- GSM9381247 Sorted Macrophages from Synovial Tissue, OA, Patient 16 Sorted Macrophages from…
- GSM9381248 Sorted Macrophages from Synovial Tissue, RA, Patient 19 Sorted Macrophages from…
- GSM9381249 Sorted Macrophages from Synovial Tissue, RA, Patient 20 Sorted Macrophages from…
- GSM9381250 Sorted Macrophages from Synovial Tissue, OA, Patient 21 Sorted Macrophages from…
- GSM9381251 Sorted Macrophages from Synovial Tissue, OA, Patient 22 Sorted Macrophages from…
- GSM9381252 Sorted Macrophages from Synovial Tissue, OA, Patient 24 Sorted Macrophages from…
- GSM9381253 Sorted Macrophages from Synovial Tissue, RA, Patient 27 Sorted Macrophages from…
- GSM9381254 Sorted Macrophages from Synovial Tissue, RA, Patient 42 Sorted Macrophages from…
- GSM9381255 Sorted Macrophages from Synovial Tissue, RA, Patient 43 Sorted Macrophages from…
- GSM9381256 Sorted Macrophages from Synovial Tissue, OA, Patient 46 Sorted Macrophages from…
- GSM9381257 Sorted Macrophages from Synovial Tissue, OA, Patient 48 Sorted Macrophages from…
- GSM9381258 Sorted Macrophages from Synovial Tissue, RA, Patient 51 Sorted Macrophages from…
- GSM9381259 Sorted Macrophages from Synovial Tissue, OA, Patient 52 Sorted Macrophages from…
- GSM9381260 Sorted Macrophages from Synovial Tissue, OA, Patient 53 Sorted Macrophages from…
- GSM9381261 Sorted Macrophages from Synovial Tissue, RA, Patient 55 Sorted Macrophages from…
- GSM9381262 Sorted Macrophages from Synovial Tissue, RA, Patient 56 Sorted Macrophages from…
- GSM9381263 Sorted Macrophages from Synovial Tissue, RA, Patient 57 Sorted Macrophages from…
- GSM9381264 Sorted Macrophages from Synovial Tissue, RA, Patient 59 Sorted Macrophages from…
- GSM9381265 Sorted Macrophages from Synovial Tissue, RA, Patient 60 Sorted Macrophages from…
- GSM9381266 Sorted Macrophages from Synovial Tissue, RA, Patient 62 Sorted Macrophages from…
- GSM9381267 Sorted Macrophages from Synovial Tissue, RA, Patient 65 Sorted Macrophages from…
- GSM9381268 Sorted Macrophages from Synovial Tissue, RA, Patient 66 Sorted Macrophages from…
- GSE314078 Transcriptional Profiling of Synovial Macrophages using Minimally Invasive Ultrasound-Guided Synovial Biopsies in Rheumatoid Arthritis [dataset1] 18 samples shares ultrasound-guided, macrophages, rheumatoid, minimally, arthritis, synovial, invasive
- GSE124928 Transcriptomic profiling of osteoarthritis synovial macrophages reveals a tolerized phenotype compounded by a weak corticosteroid response 48 samples shares macrophages, arthritis, synovial
- GSE246421 Loss of synovial tissue macrophage homeostasis precedes Rheumatoid Arthritis clinical onset 26 samples shares rheumatoid, arthritis, synovial
- GSE253553 Two Broad Categories Overlapping With Rheumatoid Arthritis Observed in Synovial Biopsies from Patients With Juvenile Idiopathic Arthritis 24 samples shares 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
- GSE274680 Inflammation and lymphocyte activation during longitudinal progression to rheumatoid arthritis in at-risk individuals 243 samples shares rheumatoid, arthritis
- GSE274996 RNAseq analysis of human neutrophils from people with DMARD-refractory rheumatoid arthritis 48 samples shares rheumatoid, arthritis
- GSE274598 RNAseq analysis of human neutrophils from people with rheumatoid arthritis 41 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.