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Single-cell and spatial transcriptomics of A-P and D-V patterned human trunk embryoid model (hTEM)

GSE314260 Homo sapiens (human) Spatial transcriptomics 17 samples Submitted 2025/12/23 Platform GPL30173
At a glance

Spatial transcriptomics · human · 17 samples

What it is
Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism
Homo sapiens (human)
Samples
17 samples: 5 × hTEM.v3, day vs 3 × hTEM.v1, day vs 2 × hTEM.v2, dayGroups 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.
Summary (written by the submitters)
Human embryoid models enable mechanistic studies of development and disease. We generated trunk embryoids from human pluripotent stem cells that recapitulate posterior trunk formation at Carnegie stage (CS) 8-10, with patterned anterior-posterior (A-P) and dorsal-ventral (D-V) axes. These self-organizing structures comprise a ventral notochord, dorsal neural tube, floor plate and bilateral somites.
Read the full summary ↓
Genetic and chemical perturbations of SHH signaling confirmed the notochord’s central role in D-V patterning. Moreover, VANGL1/2 loss-of-function mutations recapitulated mouse phenotypes, including axial truncation and somite segmentation failure. This model enables detailed study of key developmental events that underlie posterior trunk formation and provides a promising platform for human disease modeling.
This dataset
Open GSE314260 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE314260_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1390506 and SRA study SRP656309. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × hTEM.v3, day vs 3 × hTEM.v1, day vs 2 × hTEM.v2, day

Supports a between-group comparison across 10 samples.

How we read this: 3 replicated groups read from 17 sample titles; they account for 10 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.

Samples in this study
Datasets on a similar topic

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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.