GEO series

Ehmt2 Inactivation in Pancreatic Epithelial Cells Shapes the Transcriptional Landscape and Inflammation Response of the Whole Pancreas [RNA-seq]

GSE269251 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2024/06/06 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 22 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: 22 samples: 22 samples, each with a distinct title — no replicated groupsGroups 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: Ehmt2 inactivation in pancreatic epithelial cells shapes the transcriptional landscape and inflammation response of the whole pancreasFrontiers in genetics · 2024

Summary (written by the submitters)

The Euchromatic Histone Methyl Transferase Protein 2 (EHMT2), also known as G9a, deposits transcriptionally repressive chromatin marks that play pivotal roles in the maturation and homeostasis of multiple organs.Recently, we have shown that Ehmt2 inactivation in the mouse pancreas alters growth and immune gene expression networks, antagonizing Kras-mediated pancreatic cancer initiation and promotion.

Read the full summary ↓

Here, we elucidate the essential role of Ehmt2 in maintaining a transcriptional landscape that protects organs from inflammation. Comparative RNA-seq studies between normal postnatal and young adult pancreatic tissue from Ehmt2 conditional knockout animals (Ehmt2 fl/fl ) targeted to the exocrine pancreatic epithelial cells (Pdx1-Cre and P48 Cre/+ ), reveal alterations in gene expression networks in the whole organ related to injury-inflammationrepair, suggesting an increased predisposition to damage. Thus, we induced an inflammation repair response in the Ehmt2 fl/fl pancreas and used a data science-based approach to integrate RNA-seq-derived pathways and networks, deconvolution digital cytology, and spatial transcriptomics. We also analyzed the tissue response to damage at the morphological, biochemical, and molecular pathology levels. The Ehmt2 fl/fl pancreas displays an enhanced injury-inflammation-repair response, offering insights into fundamental molecular and cellular mechanisms involved in this process. More importantly, these data show that conditional Ehmt2 inactivation in exocrine cells reprograms the local environment to recruit mesenchymal and immunological cells needed to mount an increased inflammatory response. Mechanistically, this response is an enhanced injury-inflammationrepair reaction with a small contribution of specific Ehmt2-regulated transcripts. Thus, this new knowledge extends the mechanisms underlying the role of the Ehmt2- mediated pathway in suppressing pancreatic cancer initiation and modulating inflammatory pancreatic diseases.

Published in

Ehmt2 inactivation in pancreatic epithelial cells shapes the transcriptional landscape and inflammation response of the whole pancreas

Pollin G, Mathison AJ, de Assuncao TM et al. · Frontiers in genetics 2024 · PMID 38948355 · doi:10.3389/fgene.2024.1412767

This dataset

Open GSE269251 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 GSE269251_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 PRJNA1120829 and SRA study SRP512224. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38948355) ↗

Study design

22 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 22 sample titles: 22 distinct titles with little repetition. 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

GSM8310790 ID3999.PDXCre.Adult RNA
GSM8310791 ID4015.PDXCre.Adult RNA
GSM8310792 ID3951.G9aKOPDXCre.Adult RNA
GSM8310793 ID3954.G9aKOPDXCre.Adult RNA
GSM8310794 ID3978.G9aKOPDXCre.Adult RNA
GSM8310795 5038-8_PDXCre_10dPanc RNA
GSM8310796 5036-7_PDXCre_10dPanc RNA
GSM8310797 5036-8_PDXCre_10dPanc RNA
GSM8310798 5453-4_G9aKOPDXCre_10dPanc RNA
GSM8310799 5453-5_G9aKOPDXCre_10dPanc RNA
GSM8310800 5455-5_G9aKOPDXCre_10dPanc RNA
GSM8310801 5804.PDXCre.AcutePanc RNA
GSM8310802 5805.PDXCre.AcutePanc RNA
GSM8310803 5807.PDXCre.AcutePanc RNA
GSM8310804 5817.PDXCre.AcutePanc RNA
GSM8310805 5852.G9aKOPDXCre.AcutePanc RNA
GSM8310806 5854.G9aKOPDXCre.AcutePanc RNA
GSM8310807 5839.P48Cre.AcutePanc RNA
GSM8310808 5844.P48Cre.AcutePanc RNA
GSM8310809 5901.G9aKOP48Cre.AcutePanc RNA
GSM8310810 5904.G9aKOP48Cre.AcutePanc RNA
GSM8310811 5910.G9aKOP48Cre.AcutePanc RNA

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