GEO series
The RNA-binding protein Imp1 promotes a Spdef transcriptional program and mucus fucosylation during necrotizing enterocolitis
GSE318580
Mus musculus (mouse)
RNA-seq (gene expression)
32 samples
Submitted 2026/06/02
Platform GPL24247
At a glance
RNA-seq (gene expression) · mouse · 32 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
- 32 samples: 6 conditions, mostly with about 4 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)
Background: In the United States over 10% of all neonates are born premature (less than 37 weeks gestational age), and many face complications, including necrotizing enterocolitis (NEC). NEC is the most deadly gastrointestinal disease in preterm neonates with up to 50% mortality. Since there is no cure for NEC, prevention is the best strategy.
Read the full summary ↓
Enhancing our understanding of intestinal epithelial cell (IEC) responses to NEC damage will provide novel therapeutic targets to prevent NEC. Published evidence suggests that the RNA-binding protein insulin-like growth factor 2 mRNA binding protein 1 (IMP1) plays roles in intestinal development, barrier function, and intestinal repair. Notably, however, roles for IMP1 in NEC are not defined. Goblet cells produce protective mucus in the intestine, and their mature function is dependent on the transcription factor Spdef. Emerging evidence suggests that goblet cell mucus complexity impacts barrier function and inflammation susceptibility. This study aimed to define the role of IMP1 in NEC pathogenesis using neonatal human enteroids and a model of NEC-like intestinal injury in mice with IEC-specific Imp1 overexpression and loss. Hypothesis: IMP1 expression is protective in a mouse model of NEC. Methods: This study used mice with intestinal epithelial Imp1 overexpression or loss and corresponding wildtype controls. At post-natal day 3, mice of both sexes were randomly assigned to control or NEC groups. NEC was induced with the well-established experimental NEC-like intestinal injury model, including stress, formula feeding, and hypoxia. Effects were assessed using RNA sequencing, western blotting, and immunostaining. Results: Inflammatory bacteria induced IMP1 expression in neonatal human enteroids. Mice with Imp1 overexpression incur worse intestinal damage during NEC. Pathway analysis of RNA sequencing data revealed a significant enrichment of the Spdef transcriptional network in Imp1IEC-OE during NEC. This included significant upregulation of Spdef target genes such as Agr2 and Fut2. In silico analysis predicted Imp1 binding to Spdef and mucus glycosylation mediator mRNAs. Although genotype did not affect goblet cell number, Imp1IEC-OE mice with NEC exhibited significant increases (p<0.05) in Spdef protein, genes responsible for goblet cell function (Spink4, Klk1, Tspg1) and mucus glycosylation (Gcnt3, B3gnt7, Qsox1). Ultimately, Imp1 overexpression led to increased mucus fucosylation during NEC. Conclusion: Our data indicate that during NEC, upregulation of Imp1 promotes goblet cell function via Spdef, including enhanced goblet cell maturation and mucus fucosylation.
This dataset
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.
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 GSE318580_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1419255 and SRA study SRP674966. Searching any of these in the dataset finder brings you back here.
Study design
6 conditions, mostly with about 4 replicates each
dam-fed WT ×8
formula-fed WT ×8
dam-fed KO ×4
formula-fed KO ×4
formula-fed OE ×4
dam-fed OE ×4
Supports a between-group comparison across 32 samples.
How we read this: 6 replicated groups read from 32 sample titles; they account for 32 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
- GSM9497850 dam-fed WT 1 dam-fed WT
- GSM9497851 dam-fed KO 1 dam-fed KO
- GSM9497852 dam-fed WT 2 dam-fed WT
- GSM9497853 formula-fed KO 1 formula-fed KO
- GSM9497854 formula-fed WT 1 formula-fed WT
- GSM9497855 formula-fed OE 1 formula-fed OE
- GSM9497856 formula-fed OE 2 formula-fed OE
- GSM9497857 dam-fed KO 2 dam-fed KO
- GSM9497858 formula-fed WT 2 formula-fed WT
- GSM9497859 formula-fed WT 3 formula-fed WT
- GSM9497860 formula-fed KO 2 formula-fed KO
- GSM9497861 formula-fed KO 3 formula-fed KO
- GSM9497862 formula-fed KO 4 formula-fed KO
- GSM9497863 dam-fed WT 3 dam-fed WT
- GSM9497864 dam-fed OE 1 dam-fed OE
- GSM9497865 formula-fed WT 4 formula-fed WT
- GSM9497866 formula-fed WT 5 formula-fed WT
- GSM9497867 dam-fed KO 3 dam-fed KO
- GSM9497868 dam-fed WT 4 dam-fed WT
- GSM9497869 dam-fed WT 5 dam-fed WT
- GSM9497870 dam-fed WT 6 dam-fed WT
- GSM9497871 formula-fed WT 6 formula-fed WT
- GSM9497872 dam-fed OE 2 dam-fed OE
- GSM9497873 formula-fed WT 7 formula-fed WT
- GSM9497874 dam-fed OE 3 dam-fed OE
- GSM9497875 dam-fed OE 4 dam-fed OE
- GSM9497876 formula-fed OE 3 formula-fed OE
- GSM9497877 formula-fed WT 8 formula-fed WT
- GSM9497878 formula-fed OE 4 formula-fed OE
- GSM9497879 dam-fed KO 4 dam-fed KO
- GSM9497880 dam-fed WT 7 dam-fed WT
- GSM9497881 dam-fed WT 8 dam-fed WT
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Share this dataset
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.