High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development
Spatial transcriptomics · mouse · 15 samples
- What it is
- Spatial transcriptomicsGene activity measured with its position in a tissue section.
- Organism
- Mus musculus (mouse)
- Samples
- 15 samples: 5 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
- High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial developmentNature communications · 2025
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 GSE293181_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.
Also filed as BioProject PRJNA1243314 and SRA study SRP573890. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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.
- GSM8878055 E12p5_sample_1 E12p5_sample
- GSM8878056 E12p5_sample_2 E12p5_sample
- GSM8878057 E12p5_sample_3 E12p5_sample
- GSM8878058 E13p5_sample_1 E13p5_sample
- GSM8878059 E13p5_sample_2 E13p5_sample
- GSM8878060 E13p5_sample_3 E13p5_sample
- GSM8878061 E14p5_sample_1 E14p5_sample
- GSM8878062 E14p5_sample_2 E14p5_sample
- GSM8878063 E14p5_sample_3 E14p5_sample
- GSM8878064 E15p5_sample_1 E15p5_sample
- GSM8878065 E15p5_sample_2 E15p5_sample
- GSM8878066 E15p5_sample_3 E15p5_sample
- GSM8878067 E18p5_sample_1 E18p5_sample
- GSM8878068 E18p5_sample_2 E18p5_sample
- GSM8878069 E18p5_sample_3 E18p5_sample
- GSE290975 High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer 69 samples shares high-resolution, spatial, lineage
- GSE289627 CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination 88 samples shares determination, lineage, fate
- GSE289600 CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination [Cut&Tag] 52 samples shares determination, lineage, fate
- GSE289599 CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination [ChIP-Seq] 13 samples shares determination, lineage, fate
- GSE14254 Global Mapping of Histone H3 K4 and K27 Trimethylation: Lineage Fate Determination of Differentiating CD4+ T Cells 12 samples shares determination, lineage, fate
- GSE266977 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution 983 samples shares spatiotemporal, lineage
- GSE277789 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add] 830 samples shares spatiotemporal, lineage
- GSE266496 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq] 140 samples shares spatiotemporal, lineage
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.