GEO series

Differential susceptibility to colonic ulceration in mice with genetic deletion of Ptges

GSE254848 Mus musculus (mouse) RNA-seq (gene expression) 47 samples Submitted 2024/03/01 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 47 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: 47 samples: 12 × KO,10 weeks,Sample AK vs 12 × WT,10 weeks,Sample AW vs 12 × WT,10 weeks,Sample BW vs 11 × KO,10 weeks,Sample BKGroups 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)

Prostaglandin E2(PGE2) exerts pleiotropic effects on inflammation, cancer, and maintenance of mucosal homeostasis. A global knockout (KO) of the PGE2 synthase, Ptges, results in the spontaneous development of colonic ulcer in strain A mice (A/D:KO), a phenotype that is largely absent in C57BL/6 mice (B6D:KO) with the same genetic deletion.

Read the full summary ↓

Gene expression profiling of normal colonic mucosa several weeks prior to the onset of active disease identified a number of signaling pathways that may contribute to mucosal injury in the strain A mice, including the activation of inflammatory networks and antibacterial responses. Alterations toseveral microbial species includeAkkermansia muciniphilaandBacteroides vulgatus, likely associated with dysregulation of short chain fatty acid (SCFA) synthesis. These results suggest that absence ofPtgescauses a dramatic shift in the inflammatory milieu in strain A mice, an effect thatmay result from unremitting bacterial infections, triggered in part by dysregulation of epithelial homeostasis and a subtle defect in intrinsic immune regulation.

This dataset

Open GSE254848 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 GSE254848_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 PRJNA1072070 and SRA study SRP487488. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

12 × KO,10 weeks,Sample AK vs 12 × WT,10 weeks,Sample AW vs 12 × WT,10 weeks,Sample BW vs 11 × KO,10 weeks,Sample BK

Supports a between-group comparison across 47 samples.

How we read this: 4 replicated groups read from 47 sample titles; they account for 47 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

GSM8058922 Proximal colon,AD:KO,10 weeks,Sample AK10 KO,10 weeks,Sample AK
GSM8058923 Proximal colon,AD:KO,10 weeks,Sample AK11 KO,10 weeks,Sample AK
GSM8058924 Proximal colon,AD:KO,10 weeks,Sample AK12 KO,10 weeks,Sample AK
GSM8058925 Proximal colon,AD:KO,10 weeks,Sample AK13 KO,10 weeks,Sample AK
GSM8058926 Proximal colon,AD:KO,10 weeks,Sample AK1 KO,10 weeks,Sample AK
GSM8058927 Proximal colon,AD:KO,10 weeks,Sample AK2 KO,10 weeks,Sample AK
GSM8058928 Proximal colon,AD:KO,10 weeks,Sample AK3 KO,10 weeks,Sample AK
GSM8058929 Proximal colon,AD:KO,10 weeks,Sample AK4 KO,10 weeks,Sample AK
GSM8058930 Proximal colon,AD:KO,10 weeks,Sample AK5 KO,10 weeks,Sample AK
GSM8058931 Proximal colon,AD:KO,10 weeks,Sample AK6 KO,10 weeks,Sample AK
GSM8058932 Proximal colon,AD:KO,10 weeks,Sample AK7 KO,10 weeks,Sample AK
GSM8058933 Proximal colon,AD:KO,10 weeks,Sample AK9 KO,10 weeks,Sample AK
GSM8058934 Proximal colon,AD:WT,10 weeks,Sample AW10 WT,10 weeks,Sample AW
GSM8058935 Proximal colon,AD:WT,10 weeks,Sample AW11 WT,10 weeks,Sample AW
GSM8058936 Proximal colon,AD:WT,10 weeks,Sample AW12 WT,10 weeks,Sample AW
GSM8058937 Proximal colon,AD:WT,10 weeks,Sample AW1 WT,10 weeks,Sample AW
GSM8058938 Proximal colon,AD:WT,10 weeks,Sample AW2 WT,10 weeks,Sample AW
GSM8058939 Proximal colon,AD:WT,10 weeks,Sample AW3 WT,10 weeks,Sample AW
GSM8058940 Proximal colon,AD:WT,10 weeks,Sample AW4 WT,10 weeks,Sample AW
GSM8058941 Proximal colon,AD:WT,10 weeks,Sample AW5 WT,10 weeks,Sample AW
GSM8058942 Proximal colon,AD:WT,10 weeks,Sample AW6 WT,10 weeks,Sample AW
GSM8058943 Proximal colon,AD:WT,10 weeks,Sample AW7 WT,10 weeks,Sample AW
GSM8058944 Proximal colon,AD:WT,10 weeks,Sample AW8 WT,10 weeks,Sample AW
GSM8058945 Proximal colon,AD:WT,10 weeks,Sample AW9 WT,10 weeks,Sample AW
GSM8058946 Proximal colon,B6D:KO,10 weeks,Sample BK10 KO,10 weeks,Sample BK
GSM8058947 Proximal colon,B6D:KO,10 weeks,Sample BK13 KO,10 weeks,Sample BK
GSM8058948 Proximal colon,B6D:KO,10 weeks,Sample BK1 KO,10 weeks,Sample BK
GSM8058949 Proximal colon,B6D:KO,10 weeks,Sample BK2 KO,10 weeks,Sample BK
GSM8058950 Proximal colon,B6D:KO,10 weeks,Sample BK3 KO,10 weeks,Sample BK
GSM8058951 Proximal colon,B6D:KO,10 weeks,Sample BK4 KO,10 weeks,Sample BK
GSM8058952 Proximal colon,B6D:KO,10 weeks,Sample BK5 KO,10 weeks,Sample BK
GSM8058953 Proximal colon,B6D:KO,10 weeks,Sample BK6 KO,10 weeks,Sample BK
GSM8058954 Proximal colon,B6D:KO,10 weeks,Sample BK7 KO,10 weeks,Sample BK
GSM8058955 Proximal colon,B6D:KO,10 weeks,Sample BK8 KO,10 weeks,Sample BK
GSM8058956 Proximal colon,B6D:KO,10 weeks,Sample BK9 KO,10 weeks,Sample BK
GSM8058957 Proximal colon,B6D:WT,10 weeks,Sample BW10 WT,10 weeks,Sample BW
GSM8058958 Proximal colon,B6D:WT,10 weeks,Sample BW12 WT,10 weeks,Sample BW
GSM8058959 Proximal colon,B6D:WT,10 weeks,Sample BW13 WT,10 weeks,Sample BW
GSM8058960 Proximal colon,B6D:WT,10 weeks,Sample BW1 WT,10 weeks,Sample BW
GSM8058961 Proximal colon,B6D:WT,10 weeks,Sample BW2 WT,10 weeks,Sample BW

+ 7 more — browse all 47 samples with per-sample file links →

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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.