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YAP-Driven Malignant Reprogramming of Oral Epithelial Stem Cells, bulk RNA sequencing II

GSE276782 Mus musculus (mouse) RNA-seq (gene expression) 19 samples Submitted 2024/09/09 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 19 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
19 samples: 6 × K14_E6-E7_YAP mouse vs 5 × K14_E6-E7 mouse vs 5 × Control mouse vs 3 × K14_YAP mouseGroups 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
YAP-driven malignant reprogramming of oral epithelial stem cells at single cell resolutionNature communications · 2025
Summary (written by the submitters)
Bulk RNA sequencing of tongue epithelia from control mice or transgenic mice expressing HPV16E6-E7 and/or YAP1S127A
Published in
YAP-driven malignant reprogramming of oral epithelial stem cells at single cell resolution
Faraji F, Ramirez SI, Clubb LM et al. · Nature communications 2025 · PMID 39779672 · doi:10.1038/s41467-024-55660-6
This dataset
Open GSE276782 in finder → Find more mouse 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 GSE276782_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: 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 PRJNA1158847 and SRA study SRP531673. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39779672) ↗
Study design
6 × K14_E6-E7_YAP mouse vs 5 × K14_E6-E7 mouse vs 5 × Control mouse vs 3 × K14_YAP mouse

Supports a between-group comparison across 19 samples.

How we read this: 4 replicated groups read from 19 sample titles; they account for 19 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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