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IL-1R signaling drives enteric glia-macrophage interaction in colorectal cancer progression [bulkRNA-Seq]

GSE231802 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2024/06/21 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 36 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
36 samples: 9 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.
Paper
IL-1R signaling drives enteric glia-macrophage interactions in colorectal cancerNature communications · 2024
Summary (written by the submitters)
To examine the mechanisms by which EGCs affect the immune CRC compartment with particular regard to the TAMs, we first investigated their transcriptional adaptations upon CRC onset. To this end, we established an in vitro setup to study EGC-CRC interactions able to mimic the response of EGCs to the factors secreted by the TME. These EGCs, from now onwards defined as TME-conditioned medium-treated EGCs (TME-CM EGCs), were generated by stimulating primary EGCs with the CM of digested murine MC38 orthotopic tumor tissues (Figure 2A).
Read the full summary ↓
Bulk RNA sequencing (RNA-seq) was performed to determine transcriptional differences in TME-CM EGCs, compared to unstimulated and healthy conditioned medium-treated (H-CM) primary EGCs, at different time points.
Published in
IL-1R signaling drives enteric glia-macrophage interactions in colorectal cancer
van Baarle L, De Simone V, Schneider L et al. · Nature communications 2024 · PMID 39030280 · doi:10.1038/s41467-024-50438-2
This dataset
Open GSE231802 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 GSE231802_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 PRJNA967709 and SRA study SRP436172. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39030280) ↗
Study design
9 conditions, mostly with about 4 replicates each
EGCs, unstimulated, 6h, ×4 EGCs, healthy conditioned medium, 6h, ×4 EGCs, tumor conditioned medium, 6h, ×4 EGCs, unstimulated, 12h, ×4 EGCs, healthy conditioned medium, 12h, ×4 EGCs, tumor conditioned medium, 12h, ×4 EGCs, unstimulated, 24h, ×4 EGCs, healthy conditioned medium, 24h, ×4 +1 more

Supports a case/control comparison: 12 samples read as cases, 12 as controls.

How we read this: 9 replicated groups read from 36 sample titles; they account for 36 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
Datasets on a similar topic

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