Spatially resolved transcriptional landscape of human knee cartilage in patients with osteoarthritis (OA) and non-OA controls
RNA-seq (gene expression) · human · 124 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
- 124 samples
- 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.
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 GSE254844_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 PRJNA1072062 and SRA study SRP487492. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 124 more — browse all 124 samples with per-sample file links →
- GSE265899 Spatially resolved whole-transcriptomic and proteomic profiling of lung cancer and immune-microenvironment according to PD-L1 expression 95 samples shares spatially, resolved
- GSE270680 A spatially resolved atlas of gastric cancer characterises a lymphocyte aggregated region [scRNA-seq] 77 samples shares spatially, resolved
- GSE274018 Single-cell Transcriptome and Crosstalk Analysis Reveals Immune Alterations and Key Pathways in the Bone Marrow of Knee Osteoarthritis Patients 77 samples shares osteoarthritis, knee
- GSE283079 Bulk RNA-seq of human knee osteoarthritis synovium 41 samples shares osteoarthritis, knee
- GSE176078 A single-cell and spatially resolved atlas of human breast cancers 26 samples shares spatially, resolved
- GSE271045 Spatially resolved multi-bait mapping of stress granule and processing body transcriptome 24 samples shares spatially, resolved
- GSE231848 Simulated microgravity recapitulates early molecular events and sex differences of knee osteoarthritis 24 samples shares osteoarthritis, knee
- GSE253198 Cell and Transcriptomic Diversity of Infrapatellar Fat Pad during Knee Osteoarthritis [snRNA-seq] 21 samples shares osteoarthritis, knee
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.