GEO series

RNA-sequencing analysis of colon RNA from mice with compound mutations of XBP1, caspase-8, TNFR1 and MLKL.

GSE244320 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2025/08/20 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 30 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: 30 samples: 6 conditions, mostly with about 5 replicates eachGroups 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 purpose of this study was to assess how intestinal epithelial cell (IEC)-specific ablation of XBP1 or caspase-8 alone or in combination affected mucosal immune homeostastis and inflammation, and the role of TNFR1 and MLKL in the associated phenotypes. First, expression of colonic RNA from mice with combined IEC-specific XBP1 and caspase-8 ablation (Xbp1IEC-KO Casp8IEC-KO) was compared with Casp8IEC-KO, Xbp1IEC-KO, and wild-type mice.

Read the full summary ↓

In addition, Xbp1IEC-KO Casp8IEC-KO Mlkl-/- and Xbp1IEC-KO Casp8IEC-KO Tnfr1IEC-KO mice were compared with Xbp1IEC-KO Casp8IEC-KO, Casp8IEC-KO, Xbp1IEC-KO as well as wild-type control mice. For each mouse line 5 individual mice were analysed.

This dataset

Open GSE244320 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 GSE244320_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 PRJNA1022402 and SRA study SRP463838. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly with about 5 replicates each

Casp8IEC-KO, ×5 XBP1IEC-KO;Casp8IEC-KO;TNFR1IEC-KO, ×5 XBP1IEC-KO, ×5 XBP1IEC-KO;Casp8IEC-KO, ×5 XBP1IEC-KO;Casp8IEC-KO;MLKLKO, ×5 WT, ×5

Supports a between-group comparison across 30 samples.

How we read this: 6 replicated groups read from 30 sample titles; they account for 30 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

GSM7813479 Casp8IEC-KO, rep1 Casp8IEC-KO,
GSM7813480 Casp8IEC-KO, rep2 Casp8IEC-KO,
GSM7813481 Casp8IEC-KO, rep3 Casp8IEC-KO,
GSM7813482 Casp8IEC-KO, rep4 Casp8IEC-KO,
GSM7813483 Casp8IEC-KO, rep5 Casp8IEC-KO,
GSM7813484 XBP1IEC-KO;Casp8IEC-KO;TNFR1IEC-KO, rep1 XBP1IEC-KO;Casp8IEC-KO;…
GSM7813485 XBP1IEC-KO;Casp8IEC-KO;TNFR1IEC-KO, rep2 XBP1IEC-KO;Casp8IEC-KO;…
GSM7813486 XBP1IEC-KO;Casp8IEC-KO;TNFR1IEC-KO, rep3 XBP1IEC-KO;Casp8IEC-KO;…
GSM7813487 XBP1IEC-KO;Casp8IEC-KO;TNFR1IEC-KO, rep4 XBP1IEC-KO;Casp8IEC-KO;…
GSM7813488 XBP1IEC-KO;Casp8IEC-KO;TNFR1IEC-KO, rep5 XBP1IEC-KO;Casp8IEC-KO;…
GSM7813489 XBP1IEC-KO, rep1 XBP1IEC-KO,
GSM7813490 XBP1IEC-KO, rep2 XBP1IEC-KO,
GSM7813491 XBP1IEC-KO, rep3 XBP1IEC-KO,
GSM7813492 XBP1IEC-KO, rep4 XBP1IEC-KO,
GSM7813493 XBP1IEC-KO, rep5 XBP1IEC-KO,
GSM7813494 XBP1IEC-KO;Casp8IEC-KO, rep1 XBP1IEC-KO;Casp8IEC-KO,
GSM7813495 XBP1IEC-KO;Casp8IEC-KO, rep2 XBP1IEC-KO;Casp8IEC-KO,
GSM7813496 XBP1IEC-KO;Casp8IEC-KO, rep3 XBP1IEC-KO;Casp8IEC-KO,
GSM7813497 XBP1IEC-KO;Casp8IEC-KO, rep4 XBP1IEC-KO;Casp8IEC-KO,
GSM7813498 XBP1IEC-KO;Casp8IEC-KO, rep5 XBP1IEC-KO;Casp8IEC-KO,
GSM7813499 XBP1IEC-KO;Casp8IEC-KO;MLKLKO, rep1 XBP1IEC-KO;Casp8IEC-KO;…
GSM7813500 XBP1IEC-KO;Casp8IEC-KO;MLKLKO, rep2 XBP1IEC-KO;Casp8IEC-KO;…
GSM7813501 XBP1IEC-KO;Casp8IEC-KO;MLKLKO, rep3 XBP1IEC-KO;Casp8IEC-KO;…
GSM7813502 XBP1IEC-KO;Casp8IEC-KO;MLKLKO, rep4 XBP1IEC-KO;Casp8IEC-KO;…
GSM7813503 XBP1IEC-KO;Casp8IEC-KO;MLKLKO, rep5 XBP1IEC-KO;Casp8IEC-KO;…
GSM7813504 WT, rep1 WT,
GSM7813505 WT, rep2 WT,
GSM7813506 WT, rep3 WT,
GSM7813507 WT, rep4 WT,
GSM7813508 WT, rep5 WT,

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GSE201013 Effects of TNFR1 deletion on gene expression in mouse colonoic epithelial organoids 6 samples shares tnfr1, colon
GSE218955 Regulation of IkB kinase family crosstalk by an N4BP1-caspase-8 axis [RNA-seq NGS3611] 54 samples shares caspase-8
GSE304254 STING induces ZBP1-mediated necroptosis independently of TNFR1 and FADD 53 samples shares tnfr1
GSE293219 Adipocyte-specific Mlkl knockout mitigates obesity-induced metabolic dysfunction by enhancing mitochondrial functions. 36 samples shares mlkl
GSE218956 Regulation of IkB kinase family crosstalk by an N4BP1-caspase-8 axis [RNA-seq NGS3799] 36 samples shares caspase-8

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