GEO series

Single cell multiomics unravel the transcription networks controlling the different EMT tumor states

GSE288137 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2026/06/07 Platform GPL24676Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 16 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: 16 samples: 8 × SC vs 4 × MUGroups 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)

Epithelial-to-mesenchymal transition (EMT) is a process by which cells lose their epithelial characteristics and acquire mesenchymal traits. In cancer, EMT is associated with tumor initiation, progression, invasion, metastasis and resistance to therapy. Recent studies demonstrated that EMT is not a binary switch, but presents intermediate states associated with different tumor functions.

Read the full summary ↓

The gene regulatory networks (GRNs) controlling the different EMT states remain elusive. Here, using multi-OMIC approaches combining single cell RNA-seq and single cell ATAC-seq, we define the transcriptomic and chromatin landscape associated with the distinct EMT states in mouse skin squamous cell carcinoma (SCC) exhibiting EMT. Using CRISPR/Cas9-mediated loss of function studies combined with functional characterization in vitro and in vivo, we unravel the cellular and molecular mechanisms regulated by Pitx1, Klf5, Nfatc1 and Creb3l1, transcription factors (TFs) controlling specific EMT states. Altogether, our results identify the transcriptional and chromatin landscape of the distinct EMT tumor states and uncover novel key TFs controlling these states and their transition, providing potential novel targets for anti-cancer therapy.

This dataset

Open GSE288137 in finder → Find more 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 GSE288137_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: 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 PRJNA1216265 and SRA study SRP560232. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 × SC vs 4 × MU

Supports a between-group comparison across 12 samples.

How we read this: 2 replicated groups read from 16 sample titles; they account for 12 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

GSM8759594 SC2 SC
GSM8759595 SC3 SC
GSM8759596 SC1 SC
GSM8759597 SC4 SC
GSM8759598 SC5 SC
GSM8759599 SC6 SC
GSM8759600 SC7 SC
GSM8759601 SC8 SC
GSM8759602 MU1 MU
GSM8759603 MU2 MU
GSM8759604 MU3 MU
GSM8759605 MU4 MU
GSM9186413 Breast tumour sample SC9 (tumour cells)
GSM9210517 PDX human in mouse tumor resection sample, GEX modality
GSM9210518 PDX human in mouse tumor resection sample, GEX modality [PDX1_rna]
GSM9210519 PDX human in mouse tumor resection sample, ATAC modality [PDX1_atac]

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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.