A human organoid drug screen identifies α2-adrenergic receptor signaling as a therapeutic target for cartilage regeneration
RNA-seq (gene expression) · human · 22 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
- 22 samples: 6 conditions, mostly in triplicateGroups 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
- A human organoid drug screen identifies α2-adrenergic receptor signaling as a therapeutic target for cartilage regenerationCell stem cell · 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 GSE271815_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 PRJNA1133672 and SRA study SRP518819. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 3 samples read as cases, 8 as controls.
How we read this: 6 replicated groups read from 22 sample titles; they account for 18 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.
- GSM7928715 COL2+COL10- biol rep 1 COL2+COL10- biol
- GSM7928716 COL2+COL10- biol rep 2 COL2+COL10- biol
- GSM7928717 COL2+COL10- biol rep 3 COL2+COL10- biol
- GSM7928718 COL2+COL10+ biol rep 1 COL2+COL10+ biol
- GSM7928719 COL2+COL10+ biol rep 2 COL2+COL10+ biol
- GSM7928720 COL2+COL10+ biol rep 3 COL2+COL10+ biol
- GSM7928721 D42 vehicle pellets biol rep 1 D42 vehicle pellets biol
- GSM7928722 D42 vehicle pellets biol rep 2 D42 vehicle pellets biol
- GSM7928723 D42 vehicle pellets biol rep 3 D42 vehicle pellets biol
- GSM7928724 D42 PM treated pellets rep 1 D42 PM treated pellets
- GSM7928725 D42 PM treated pellets rep 2 D42 PM treated pellets
- GSM7928726 D42 PM treated pellets rep 3 D42 PM treated pellets
- GSM7928727 D42 control pellets rep 1 D42 control pellets
- GSM7928728 D42 control pellets rep 2 D42 control pellets
- GSM7928729 D42 control pellets rep 3 D42 control pellets
- GSM7928730 D42 SLPI KO pellets rep 1 D42 SLPI KO pellets
- GSM7928731 D42 SLPI KO pellets rep 2 D42 SLPI KO pellets
- GSM7928732 D42 SLPI KO pellets rep 3 D42 SLPI KO pellets
- GSM8385872 CTRL_1,scRNAseq
- GSM8385873 CTRL_2,scRNAseq
- GSM8385874 PM_1,scRNAseq
- GSM8385875 PM_2,scRNAseq
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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.