Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq]
Single-cell RNA-seq · mouse · 140 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 140 samples: 140 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
- Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolutionCell · 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 GSE266496_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 PRJNA1107394 and SRA study SRP506206. 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 140 sample titles: 140 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.
- GSM8248220 Endoderm Hhex 09ss b1, scRNA-seq
- GSM8248221 Endoderm Hhex 09ss b2, scRNA-seq
- GSM8248222 Endoderm Hhex 12ss b1, scRNA-seq
- GSM8248223 Endoderm Hhex 12ss b2, scRNA-seq
- GSM8248224 Endoderm Hhex 15ss b1, scRNA-seq
- GSM8248225 Endoderm Hhex 15ss b2, scRNA-seq
- GSM8248226 Endoderm Hhex 18ss b1, scRNA-seq
- GSM8248227 Endoderm Hhex 18ss b2, scRNA-seq
- GSM8248228 Endoderm Hhex 21ss b1, scRNA-seq
- GSM8248229 Endoderm Hhex 21ss b2, scRNA-seq
- GSM8248230 Endoderm Hhex 24ss b1, scRNA-seq
- GSM8248231 Endoderm Hhex 24ss b2, scRNA-seq
- GSM8248232 Endoderm Hhex 27ss b1, scRNA-seq
- GSM8248233 Endoderm Hhex 27ss b2, scRNA-seq
- GSM8248234 Endoderm Mnx1 09ss b1, scRNA-seq
- GSM8248235 Endoderm Mnx1 09ss b2, scRNA-seq
- GSM8248236 Endoderm Mnx1 12ss b1, scRNA-seq
- GSM8248237 Endoderm Mnx1 12ss b2, scRNA-seq
- GSM8248238 Endoderm Mnx1 15ss b1, scRNA-seq
- GSM8248239 Endoderm Mnx1 15ss b2, scRNA-seq
- GSM8248240 Endoderm Mnx1 18ss b1, scRNA-seq
- GSM8248241 Endoderm Mnx1 18ss b2, scRNA-seq
- GSM8248242 Endoderm Mnx1 21ss b1, scRNA-seq
- GSM8248243 Endoderm Mnx1 21ss b2, scRNA-seq
- GSM8248244 Endoderm Mnx1 24ss b1, scRNA-seq
- GSM8248245 Endoderm Mnx1 24ss b2, scRNA-seq
- GSM8248246 Endoderm Mnx1 27ss b1, scRNA-seq
- GSM8248247 Endoderm Mnx1 27ss b2, scRNA-seq
- GSM8248248 Endoderm Mnx1GFP 09ss b1, scRNA-seq
- GSM8248249 Endoderm Mnx1GFP 09ss b2, scRNA-seq
- GSM8248250 Endoderm Mnx1GFP 12ss b1, scRNA-seq
- GSM8248251 Endoderm Mnx1GFP 12ss b2, scRNA-seq
- GSM8248252 Endoderm Mnx1GFP 15ss b1, scRNA-seq
- GSM8248253 Endoderm Mnx1GFP 15ss b2, scRNA-seq
- GSM8248254 Endoderm Mnx1GFP 18ss b1, scRNA-seq
- GSM8248255 Endoderm Mnx1GFP 18ss b2, scRNA-seq
- GSM8248256 Endoderm Mnx1GFP 21ss b1, scRNA-seq
- GSM8248257 Endoderm Mnx1GFP 21ss b2, scRNA-seq
- GSM8248258 Endoderm Mnx1GFP 24ss b1, scRNA-seq
- GSM8248259 Endoderm Mnx1GFP 24ss b2, scRNA-seq
+ 100 more — browse all 140 samples with per-sample file links →
- GSE277789 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add] 830 samples shares smart-seq3-rna-seq, spatiotemporal, organogenesis, single-cell, endodermal, resolution, genetic, lineage
- GSE266497 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [10x-v3-RNA-seq] 13 samples shares spatiotemporal, organogenesis, single-cell, endodermal, resolution, genetic, lineage
- GSE150817 Transcriptional dynamics of the murine heart during perinatal development at single-cell resolution 30 samples shares single-cell, resolution
- GSE310028 Dissecting Semaglutide-dependent transcriptome response in obesity and osteoarthritis across tissues at single-cell resolution 28 samples shares single-cell, resolution
- GSE227108 Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells (scRNA-seq) 18 samples shares single-cell, genetic
- GSE249931 Temporal single-cell profiling of distinct mesenchymal, epithelial, endothelial, and immune cell lineages in the lung after injury 17 samples shares single-cell, lineage
- GSE303460 Spatiotemporal single-cell atlas of suture stem cell dynamics in craniosynostosis [scRNA-Seq] 14 samples shares spatiotemporal, single-cell
- GSE294795 Hypertension-Induced Neurovascular and Cognitive Dysfunction at Single-Cell Resolution 12 samples shares single-cell, resolution
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.