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DSS chronic colitis induces osteoporosis by changing osteal macrophages to an inflammatory phenotype.

GSE295136 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/03/15 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 3 × Osteal macrophage stimulated by 3%DSS 1weeks vs 3 × Osteal macrophage stimulated by 3%DSS 3weeks vs 3 × Osteal macrophage stimulated by LPS vs 3 × Osteal macrophage not stimulatedGroups 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)
Osteal macrophages are bone-resident macrophages.In this study, we investigated the functional properties of Osteal macrophages in osteoporosis caused by chronic colitis. In this study, we investigated the functional properties of Osteal macrophage in osteoporosis caused by chronic colitis.We found that Osteal macrophages are altered in an inflammatory manner and affect osteoblast and osteoclast differentiation.
Read the full summary ↓
To understand this mechanism, we isolated and collected Osteal macrophages from mice with DSS-induced colitis and comprehensively analyzed changes in gene expression by bulk RNA analysis
This dataset
Open GSE295136 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 GSE295136_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 PRJNA1253592 and SRA study SRP580331. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × Osteal macrophage stimulated by 3%DSS 1weeks vs 3 × Osteal macrophage stimulated by 3%DSS 3weeks vs 3 × Osteal macrophage stimulated by LPS vs 3 × Osteal macrophage not stimulated

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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