Retinoic acid promotes tissue regeneration by resolving stem cell lineage plasticity
RNA-seq (gene expression) · mouse · 27 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
- Mus musculus (mouse)
- Samples
- 27 samples: 27 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
- Vitamin A resolves lineage plasticity to orchestrate stem cell lineage choicesScience (New York, N.Y.) · 2024
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 GSE231731_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 PRJNA967382 and SRA study SRP435987. 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 27 sample titles: 27 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.
- GSM7299724 AnaVI (P32) skin mouse 1, scRNA-seq
- GSM7299725 AnaVI (P32) skin mouse 2, scRNA-seq
- GSM7299726 Cultured HFSCs mouse 1, scRNA-seq
- GSM7299727 Cultured HFSCs mouse 1, HTO
- GSM7299728 Cultured HFSCs mouse 2, scRNA-seq
- GSM7299729 Cultured HFSCs mouse 2, HTO
- GSM8120996 Rxra cKO FBS HFSCs 1, ATAC-seq
- GSM8120997 Rxra cKO FBS HFSCs 2, ATAC-seq
- GSM8120998 Rxra cKO atRA+PKCi HFSCs 1, ATAC-seq
- GSM8120999 Rxra cKO atRA+PKCi HFSCs 2, ATAC-seq
- GSM8121000 wild-type FBS HFSCs 1, ATAC-seq
- GSM8121001 wild-type FBS HFSCs 2, ATAC-seq
- GSM8121002 wild-type atRA+PKCi HFSCs 1, ATAC-seq
- GSM8121003 wild-type atRA+PKCi HFSCs 2, ATAC-seq
- GSM8121004 Rxra cKO FBS HFSCs 1, RNA-seq
- GSM8121005 Rxra cKO FBS HFSCs 2, RNA-seq
- GSM8121006 Rxra cKO atRA+PKCi HFSCs 1, RNA-seq
- GSM8121007 Rxra cKO atRA+PKCi HFSCs 2, RNA-seq
- GSM8121008 wild-type FBS HFSCs 1, RNA-seq
- GSM8121009 wild-type FBS HFSCs 2, RNA-seq
- GSM8121010 wild-type atRA+PKCi HFSCs 1, RNA-seq
- GSM8121011 wild-type atRA+PKCi HFSCs 2, RNA-seq
- GSM8121012 HFSCs, CNR IgG
- GSM8121013 HFSCs 1, CNR Rarg
- GSM8121014 HFSCs 2, CNR Rarg
- GSM8121015 HFSCs 1, CNR Rxra
- GSM8121016 HFSCs 2, CNR Rxra
- GSE288156 Progressive intestinal tumor cell plasticity, Myc activation and loss of Lgr5+ tumor stem cell lineage commitment upon Wnt depletion 14 samples shares plasticity, lineage, stem
- GSE309033 Combined BET Bromodomain and DNMT Inhibition Targets Lineage Plasticity in Prostate Cancer [BETi_DNMTi_mouse_RNAseq] 51 samples shares plasticity, lineage
- GSE226579 Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration [RNA-seq] 47 samples shares regeneration, stem
- GSE269634 Triggering AHR resolves TGF-β1 induced fibroblast activation and promotes AT1 cell regeneration in alveolar organoids 32 samples shares regeneration, promotes
- GSE247505 Sustained NF-kB activation allows mutant alveolar stem cells to co-opt a regeneration program for tumor initiation 20 samples shares regeneration, stem
- GSE266900 Cxcr3 promotes protection from colorectal cancer liver metastasis by driving NK infiltration and plasticity 18 samples shares plasticity, promotes
- GSE301448 Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuroregeneration [RNAseq-Stroke] 18 samples shares regeneration, promotes
- GSE284043 RNAseq for peritoneal macrophages phagocytosing E.coli in the absence or presence of retinoic acid 16 samples shares retinoic, acid
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.