GEO series

ADAMTS7 promotes smooth muscle foam cell expansion in atherosclerosis

GSE316135 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2026/01/16 Platform GPL34475Platform GPL34290

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 10 samples: 10 samples, each with a distinct title — no replicated groupsGroups 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: ADAMTS7 Promotes Smooth Muscle Foam Cell Expansion in AtherosclerosisbioRxiv : the preprint server for biology · 2024

Summary (written by the submitters)

Human genetic studies have repeatedly associated ADAMTS7 with atherosclerotic cardiovascular disease. Subsequent investigations in mice demonstrated that ADAMTS7 is proatherogenic and induced in response to vascular injury and that the proatherogenicity of ADAMTS7, a secreted protein, is due to its catalytic activity. However, the cell-specific mechanisms governing ADAMTS7 proatherogenicity remain unclear.

Read the full summary ↓

To determine which vascular cell types express ADAMTS7, we interrogated single-cell RNA sequencing of human carotid atherosclerosis and found ADAMTS7 expression in smooth muscle cells (SMCs), endothelial cells (ECs), and fibroblasts. We subsequently created SMC- and EC-specific Adamts7 conditional knockout and transgenic mice. Conditional knockout of Adamts7 in either cell type is insufficient to reduce atherosclerosis, whereas transgenic induction in either cell type increases atherosclerosis. In SMC transgenic mice, this increase coincides with an expansion of lipid-laden SMC foam cells and decreased fibrous cap formation. RNA-sequencing in SMCs revealed an upregulation of lipid uptake genes typically assigned to macrophages. Subsequent experiments demonstrated that ADAMTS7 increases SMC oxLDL uptake through increased CD36 levels. Furthermore, Cd36 expression is increased due to increased levels of PU.1, a transcription factor typically associated with myeloid fate determination. In summary, Adamts7 expression in either SMCs or ECs promotes SMC foam cell formation and atherosclerosis. In SMCs, ADAMTS7 promotes oxLDL uptake via increased PU.1 and Cd36 expression, thereby increasing SMC foam cell formation and atherosclerosis.

Published in

ADAMTS7 Promotes Smooth Muscle Foam Cell Expansion in Atherosclerosis

Chung A, Chang HK, Pan H et al. · bioRxiv : the preprint server for biology 2024 · PMID 38463994 · doi:10.1101/2024.02.26.582156

This dataset

Open GSE316135 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 GSE316135_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1401693 and SRA study SRP661420. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38463994) ↗

Study design

10 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 2 samples read as cases, 5 as controls.

How we read this: Read from 10 sample titles: 10 distinct titles with little repetition. 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

GSM9445376 WT VSMCs, mouse 1, ATAC
GSM9445377 WT VSMCs, mouse 2, ATAC
GSM9445378 Adamts7 VSMC specific overexpression, mouse 1, ATAC
GSM9445379 Adamts7 VSMC specific overexpression, mouse 2, ATAC
GSM9445380 WT VSMCs, mouse 1, RNA
GSM9445381 WT VSMCs, mouse 2, RNA
GSM9445382 WT VSMCs, mouse 3, RNA
GSM9445383 WT VSMC specific overexpression, mouse 1, RNA
GSM9445384 WT VSMC specific overexpression, mouse 2, RNA
GSM9445385 WT VSMC specific overexpression, mouse 3, RNA

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