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RNA-sequencing reveals novel molecular mechanisms of endometriosis lesion development in a mouse model

GSE255418 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2024/10/17 Platform GPL19057
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
RNA sequencing reveals molecular mechanisms of endometriosis lesion development in miceDisease models & mechanisms · 2024
Summary (written by the submitters)
Our understanding of molecular mechanisms contributing to the pathophysiology of endometriosis, and their upstream regulators, remains limited. Using a C57Bl/6 mouse model of endometriosis in which decidualized endometrial tissue fragments are transferred to subcutaneous sites in recipient mice to mimic endometriosis lesions, we have generated a comprehensive profile of gene expression in decidualized endometrial tissue (n=4), and endometriosis-like lesions at Day 7 (n=4) and Day 14 (n=4) of lesion formation.
Read the full summary ↓
High throughput mRNA sequencing allowed identification of genes and pathways involved in the initiation and progression of endometriosis-like lesions. We found distinct patterns of gene expression with substantial differences between the lesions and the decidualized endometrium from which they arose, but no differentially expressed genes between the two lesion timepoints. The transcriptional changes at the outset of lesion formation indicated substantial upregulation of immune response-associated canonical pathways. Pathway enrichment analysis indicates multiple potential endogenous upstream regulators, and reveals multiple gene candidates not previously implicated in endometriosis lesion formation suggesting these mediators may have novel roles in disease progression. Collectively, the provided data will be a valuable resource to inform research on the molecular mechanisms contributing to endometriosis development.
Published in
RNA sequencing reveals molecular mechanisms of endometriosis lesion development in mice
Panir K, Schjenken JE, Breen J et al. · Disease models & mechanisms 2024 · PMID 39385609 · doi:10.1242/dmm.050566
This dataset
Open GSE255418 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 GSE255418_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 PRJNA1074834 and SRA study SRP489046. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39385609) ↗
Study design
9 conditions, mostly with about 4 replicates each
C57BL/6, decidualized endometrium, ×4 C57BL/6, D7 endometriosis lesion, ×4 C57BL/6, D14 endometriosis lesion, ×4 miR155, decidualized endometrium, ×4 miR155, D7 endometriosis lesion, ×4 miR155, D14 endometriosis lesion, ×4 miR223, decidualized endometrium, ×4 miR223, D7 endometriosis lesion, ×4 +1 more

Supports a between-group comparison across 36 samples.

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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