Novel ex vivo culture of purified mouse mesenchymal stromal cells reveals tissue-dependent niche heterogeneity in bone marrow and functional interaction with macrophages
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 × BM_Sorted vs 3 × BM_NonSorted vs 3 × BAC_Depleted vs 3 × BAC_NonDepletedGroups 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
- Monocytes/macrophages contamination disrupts functional and transcriptional characteristics of murine bone marrow- and bone-derived stromal cellsJBMR plus · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE228749_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA951395 and SRA study SRP430486. Searching any of these in the dataset finder brings you back here.
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.
- GSM7135818 BM_Sorted_1 BM_Sorted
- GSM7135819 BM_Sorted_2 BM_Sorted
- GSM7135820 BM_Sorted_3 BM_Sorted
- GSM7135821 BM_NonSorted_1 BM_NonSorted
- GSM7135822 BM_NonSorted_2 BM_NonSorted
- GSM7135823 BM_NonSorted_3 BM_NonSorted
- GSM7135824 BAC_Depleted_1 BAC_Depleted
- GSM7135825 BAC_Depleted_2 BAC_Depleted
- GSM7135826 BAC_Depleted_3 BAC_Depleted
- GSM7135827 BAC_NonDepleted_1 BAC_NonDepleted
- GSM7135828 BAC_NonDepleted_2 BAC_NonDepleted
- GSM7135829 BAC_NonDepleted_3 BAC_NonDepleted
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- GSE302734 Single-Cell RNA Sequencing Unravels Interactions between Macrophages and Fibroadipogenic Progenitors during Ectopic Bone Formation in FOP Mice 12 samples shares interaction, macrophages
- GSE293493 Transcriptional effects of co-culture on the spatiotemporal dynamics of T cell motility and cancer-T cell interactions [bulk_seq_IFN] 10 samples shares interaction, culture
- GSE269027 Complex interaction of tumor-derived factors instructs the niche specific phenotypes of tumor-associated macrophages (in vitro ATAC-Seq) 27 samples shares interaction, macrophages
- GSE290434 A stress response axis in tumor-associated macrophages dictates phenotype heterogeneity and immunotherapy evasion 21 samples shares heterogeneity, macrophages
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- GSE255212 Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interaction during Primordial Follicle Activation 762 samples shares interaction
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.