GEO series

MTGR1 is required to maintain small intestinal stem cell populations - RNA-sequencing

GSE270546 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2024/07/01 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 18 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: 18 samples: 6 conditions, mostly in triplicateGroups 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: MTGR1 is required to maintain small intestinal stem cell populationsCell death and differentiation · 2024

Summary (written by the submitters)

Undifferentiated intestinal stem cells (ISCs), particularly those marked by Lgr5, are crucial for maintaining homeostasis and resolving injury. Lgr5+ cells in the crypt base constantly divide, pushing daughter cells upward along the crypt axis where they differentiate into specialized cell types. Coordinated execution of complex transcriptional programs are necessary to allow for the maintenance of undifferentiated stem cells while permitting differentiation of the wide array of intestinal cells necessary for homeostasis.

Read the full summary ↓

Previously, members of the myeloid translocation gene (MTG) family have been identified as transcriptional co-repressors that regulate stem cell maintenance and differentiation programs in multiple organ systems, including the intestine. One MTG family member, myeloid translocation gene related 1 (MTGR1), has been recognized as a crucial regulator of secretory cell differentiation and response to injury. However, whether MTGR1 contributes to the function of ISCs has not yet been examined. Here, using Mtgr1-/- mice, we have assessed the effects of MTGR1 loss specifically in ISC biology. Interestingly, loss of MTGR1 increased the total number of cells expressing Lgr5, the canonical marker of cycling ISCs, suggesting higher overall stem cell numbers. However, expanded transcriptomic and functional analyses revealed deficiencies in MTGR1 null ISCs, including deregulated ISC-associated transcriptional programs. Ex vivo, intestinal organoids established from Mtgr1 null were found nearly completely unable to survive and expand, likely due to aberrant differentiation and loss of stem and proliferative cells. Together, these results indicate that MTGR1’s role in intestinal differentiation is likely to be stem cell intrinsic and identify a novel role MTGR1 in maintaining ISC function.

Published in

MTGR1 is required to maintain small intestinal stem cell populations

Short SP, Brown RE, Chen Z et al. · Cell death and differentiation 2024 · PMID 39048708 · doi:10.1038/s41418-024-01346-x

This dataset

Open GSE270546 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 GSE270546_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 PRJNA1127478 and SRA study SRP515891. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39048708) ↗

Study design

6 conditions, mostly in triplicate

WT crypt mouse ×3 Mtgr1 null crypt mouse ×3 Mtgr1 null D1 enteroid mouse ×3 WT D3 enteroid mouse ×3 Mtgr1 null D3 enteroid mouse ×3 WT D1 enteroid mouse ×2 WT D1 enteroid moue ×1

Supports a between-group comparison across 17 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 17 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

GSM8346453 WT crypt mouse 1 WT crypt mouse
GSM8346454 WT crypt mouse 2 WT crypt mouse
GSM8346455 WT crypt mouse 3 WT crypt mouse
GSM8346456 Mtgr1 null crypt mouse 1 Mtgr1 null crypt mouse
GSM8346457 Mtgr1 null crypt mouse 2 Mtgr1 null crypt mouse
GSM8346458 Mtgr1 null crypt mouse 3 Mtgr1 null crypt mouse
GSM8346459 WT D1 enteroid mouse 1 WT D1 enteroid mouse
GSM8346460 WT D1 enteroid mouse 2 WT D1 enteroid mouse
GSM8346461 WT D1 enteroid moue 3
GSM8346462 Mtgr1 null D1 enteroid mouse 1 Mtgr1 null D1 enteroid …
GSM8346463 Mtgr1 null D1 enteroid mouse 2 Mtgr1 null D1 enteroid …
GSM8346464 Mtgr1 null D1 enteroid mouse 3 Mtgr1 null D1 enteroid …
GSM8346465 WT D3 enteroid mouse 1 WT D3 enteroid mouse
GSM8346466 WT D3 enteroid mouse 2 WT D3 enteroid mouse
GSM8346467 WT D3 enteroid mouse 3 WT D3 enteroid mouse
GSM8346468 Mtgr1 null D3 enteroid mouse 1 Mtgr1 null D3 enteroid …
GSM8346469 Mtgr1 null D3 enteroid mouse 2 Mtgr1 null D3 enteroid …
GSM8346470 Mtgr1 null D3 enteroid mouse 3 Mtgr1 null D3 enteroid …

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