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Investigating the role of ERBB2 during colorectal cancer in the ApcMin/+ mouse model

GSE241084 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2024/08/16 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 20 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
20 samples: 5 × Erbb2-deficient ApcMin, tumor, biol vs 5 × Erbb2-deficient ApcMin, adjacent normal, biol vs 5 × ApcMin, tumor, biol vs 5 × ApcMin, adjacent normal, biolGroups 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)
The ERBB family consists of four receptors (EGFR, ERBB2, ERBB3, and ERBB4) that are critical in normal development and physiology of mammalian gastrointestinal epithelial tissues. Amplifications or mutations in ERBB2 are commonly found in CRC, suggesting a possible therapeutic target. Patients with ERBB2-amplification in breast and gastroesophageal cancer are routinely treated with the ERBB2-directed antibody trastuzumab.
Read the full summary ↓
However, ERBB2 is not commonly targeted in clinical practice of treating CRC. Notably, ERBB2 status could guide therapy as a negative marker for EGFR-targeted therapy (cetuximab) and identify likely responders for ERBB2-directed therapy. Although the most common marker for negative efficacy of anti-EGFR therapy is KRAS mutations, many patients with KRAS wild-type tumors do not respond to EGFR inhibition. As the primary EGFR-directed antibodies for CRC do not inhibit ERBB2, alterations increasing ERBB2 may serve as a superior negative predictor of EGFR therapy since previous studies demonstrate that ERBB2 amplification confers resistance to cetuximab in preclinical models. Despite the compelling evidence, the utility of ERBB2 as a target for molecular therapy of primary CRC tumors in preclinical models is largely unexplored. As such, our goal is to further characterize the influece of ERBB2 in the initiation and progression of CRC.
This dataset
Open GSE241084 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 GSE241084_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 PRJNA1006373 and SRA study SRP455634. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × Erbb2-deficient ApcMin, tumor, biol vs 5 × Erbb2-deficient ApcMin, adjacent normal, biol vs 5 × ApcMin, tumor, biol vs 5 × ApcMin, adjacent normal, biol

Supports a case/control comparison: 10 samples read as cases, 10 as controls.

How we read this: 4 replicated groups read from 20 sample titles; they account for 20 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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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.