Role of GPNMB in Foam Cells Formation and Atherosclerosis Progression
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 × BMDMs from control mice vs 3 × BMDMs from GpnmbR150X mice vs 3 × OxLDL-treated BMDMs from control mice vs 3 × OxLDL-treated BMDMs from GpnmbR150X miceGroups 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
- Regulation of lipoprotein processing by GPNMB in foamy macrophages: potential therapeutic targets for atherosclerosisNature communications · 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 GSE274954_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 PRJNA1148641 and SRA study SRP526730. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 3 samples read as cases, 3 as controls.
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.
- GSM8462805 BMDMs from control mice replicate 1 BMDMs from control mice
- GSM8462806 BMDMs from control mice replicate 2 BMDMs from control mice
- GSM8462807 BMDMs from control mice replicate 3 BMDMs from control mice
- GSM8462808 BMDMs from GpnmbR150X mice replicate 1 BMDMs from GpnmbR150X m…
- GSM8462809 BMDMs from GpnmbR150X mice replicate 2 BMDMs from GpnmbR150X m…
- GSM8462810 BMDMs from GpnmbR150X mice replicate 3 BMDMs from GpnmbR150X m…
- GSM8619234 OxLDL-treated BMDMs from control mice replicate 1 OxLDL-treated BMDMs fro…
- GSM8619235 OxLDL-treated BMDMs from control mice replicate 2 OxLDL-treated BMDMs fro…
- GSM8619236 OxLDL-treated BMDMs from control mice replicate 3 OxLDL-treated BMDMs fro…
- GSM8619237 OxLDL-treated BMDMs from GpnmbR150X mice replicate 1 OxLDL-treated BMDMs fro…
- GSM8619238 OxLDL-treated BMDMs from GpnmbR150X mice replicate 2 OxLDL-treated BMDMs fro…
- GSM8619239 OxLDL-treated BMDMs from GpnmbR150X mice replicate 3 OxLDL-treated BMDMs fro…
- GSE232854 Control of Mycobacterium abscessus pulmonary infection requires IFN- γ Induced formation of foam macrophages 22 samples shares formation, foam
- GSE280003 Gpnmb and Spp1 mark a conserved macrophage injury response masking fibrosis-specific programming in the lung 81 samples shares gpnmb
- GSE241770 ACSS2 mediates an epigenetic pathway to regulate maternal Beta-cell adaptation and progression of gestational diabetes (scRNA-Seq) 7899 samples shares progression
- GSE239602 Single-cell and spatial transcriptomics uncovers the role of senescent vascular cells in pathological arterial remodeling during murine atherosclerosis 82 samples shares atherosclerosis
- GSE239591 Single-cell and spatial transcriptomics uncovers the role of senescent vascular cells in pathological arterial remodeling during murine atherosclerosis 6 samples shares atherosclerosis
- GSE327470 Temporal Uncoupling of Radial Glial Progenitor Cell Lineage Progression in Self-organizing Organoid System 292 samples shares progression
- GSE327468 Temporal Uncoupling of Radial Glial Progenitor Cell Lineage Progression in Self-organizing Organoid System – MADM-CloneSeq 287 samples shares progression
- GSE159911 “Bench-to-Bedside and Back” analysis of NAFLD model reveals common transcriptomic shifts between mouse and human during disease progression 152 samples shares progression
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.