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ATF4 CDS or pas deletion in cardiomyocyte in E11.5 mouse heart RNAseq

GSE328315 Mus musculus (mouse) RNA-seq (gene expression) 15 samples Submitted 2026/05/12 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 15 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
15 samples: 4 × RNA-seq of CM-specific ATF4 CDS KO mice E11.5 heart vs 4 × RNA-seq of ATF4 CDS Control mice E11.5 heart vs 4 × RNA-seq of CM-specific ATF4 PAS KO mice E11.5 heart vs 3 × RNA-seq of ATF4 PAS Control mice E11.5 heartGroups 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)
to ivestigate whether an intact PAS independently prevents readthrough regardless of gene body context, or whether selective PAS loss alone is sufficient to trigger transcriptional termination failure. we generated two complementary mouse models at the endogenous Atf4 locus. In the first, the coding sequence was deleted while the canonical PAS and its associated auxiliary elements were preserved (Atf4 ΔCDS), isolating the contribution of gene body disruption from defects in 3′ end processing.
Read the full summary ↓
In the second, the canonical PAS and its auxiliary elements were selectively deleted while the coding sequence was fully retained (Atf4 ΔPAS), enabling direct assessment of whether loss of the full PAS regulatory module is sufficient to trigger transcriptional termination failure in vivo. The Atf4 ΔCDS model exhibits only modest transcriptional readthrough compared to the Atf4 ΔCDS+ΔPAS allele. Strikingly, selective loss of the canonical PAS does not induce detectable downstream readthrough; instead, RNAPII terminates at a cryptic upstream site within exon 3, generating truncated transcripts. These findings demonstrate that PAS loss alone is not sufficient to drive transcriptional readthrough at the endogenous Atf4 locus and reveal an unexpected plasticity in RNAPII termination site selection in vivo.
This dataset
Open GSE328315 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 GSE328315_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 PRJNA1454770 and SRA study SRP692655. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × RNA-seq of CM-specific ATF4 CDS KO mice E11.5 heart vs 4 × RNA-seq of ATF4 CDS Control mice E11.5 heart vs 4 × RNA-seq of CM-specific ATF4 PAS KO mice E11.5 heart vs 3 × RNA-seq of ATF4 PAS Control mice E11.5 heart

Supports a between-group comparison across 15 samples.

How we read this: 4 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.

Samples in this study
Datasets on a similar topic

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