GEO series
Identifying mediators of cytosolic myddosome assembly
GSE321692
Mus musculus
Expression profiling by high throughput sequencing
16 samples
Submitted 2026/08/07
Platform GPL24247
Summary
Toll-like receptor (TLR) activation induces the formation of highly dynamic myddosomes in the cytosol of macrophages. However, not all cells respond, macrophage populations consistently contain bystanders whose frequency tracks with ligand concentration and activated TLR. We established a flow cytometry–based assay to separate responder and bystander cells via SSC changes (SSClo vs SSChi) reflecting cytosolic myddosomes in immortalized bone marrow-derived macrophages (iBMDM) with endogenously-tagged MyD88 (MyD88-AGF). We performed bulk RNA-Seq to compare responder and bystander cells to untreated cells and LPS-treated but unsorted pools. Clustering and individual comparisons confirmed high similarity between responders and the LPS pool and a distinct bystander signature. Comparing bystanders to responders and untreated to LPS-treated pools showed reduced induction of TLR primary and secondary response genes (PRGs/SRGs) in bystanders, while interferon-stimulated genes (ISGs) induced via paracrine signaling remained intact. Thus, myddosome-containing cells drive the LPS-induced transcriptional program, whereas bystanders only retain IFN responsiveness.
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE321692_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 16 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1429296 and SRA study SRP679799. Searching any of these in the dataset finder brings you back here.
Study design
4 × iBMDM, 10 ng/mL LPS-treated, 6 hrs, unsorted pool, vs 4 × iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted low SSC, vs 4 × iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted high SSC, vs 4 × iBMDM, untreated control, unsorted pool,
Supports a between-group comparison across 16 samples.
4 replicated groups read from 16 sample titles; they account for 16 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9549641 iBMDM, 10 ng/mL LPS-treated, 6 hrs, unsorted pool, rep1
- GSM9549642 iBMDM, 10 ng/mL LPS-treated, 6 hrs, unsorted pool, rep2
- GSM9549643 iBMDM, 10 ng/mL LPS-treated, 6 hrs, unsorted pool, rep3
- GSM9549644 iBMDM, 10 ng/mL LPS-treated, 6 hrs, unsorted pool, rep4
- GSM9549645 iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted low SSC, rep1
- GSM9549646 iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted low SSC, rep2
- GSM9549647 iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted low SSC, rep3
- GSM9549648 iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted low SSC, rep4
- GSM9549649 iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted high SSC, rep1
- GSM9549650 iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted high SSC, rep2
- GSM9549651 iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted high SSC, rep3
- GSM9549652 iBMDM, 10 ng/mL LPS-treated, 6 hrs, sorted high SSC, rep4
- GSM9549653 iBMDM, untreated control, unsorted pool, rep1
- GSM9549654 iBMDM, untreated control, unsorted pool, rep2
- GSM9549655 iBMDM, untreated control, unsorted pool, rep3
- GSM9549656 iBMDM, untreated control, unsorted pool, rep4
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