GEO series

Polymicrobial-driven NLRP6 inflammasome regulates 1 IL-1b production and alveolar bone loss in a murine model of periodontitis

GSE339420 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2026/07/27 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 18 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: 18 samples: 8 conditions, mostly in duplicateGroups 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)

Periodontal disease is a chronic inflammatory condition that develops in response to oral microbiome dysbiosis and host-microbiome immune response dysregulation. The innate immune system plays a major role in the development and persistence of disease in part by producing inflammatory cytokines. One of the major cytokines implicated in disease is interleukin-1b (IL-1b), which requires inflammasome activation.

Read the full summary ↓

Much of the oral microbiome, including Streptococci, which are otherwise considered commensal, is required for the full development of periodontal disease. We have previously reported that inflammatory-activated macrophages and neutrophils counterintuitively allow survival of internalized Streptococcus gordonii over non-activated phagocytes. This internal bacterial survival leads to inflammasome activation via the cytoplasmic activator NLRP6, but not NLRP3, and subsequent increases in IL-1b release. Here, we test and find that the keystone pathogen Porphyromonas gingivalis can activate macrophages in a manner that allows for increased S. gordonii survival and IL-1b production above levels when P. gingivalis interacts with macrophages alone. We also use the mouse ligature-induced periodontal disease model to test the importance of NLRP6 in disease development. We found mice lacking NLRP6 had significantly reduced bone loss, IL-1b, and neutrophil infiltration following disease induced by P. gingivalis when S. gordonii or other mouse commensals were present, but had no effect when S. gordonii was inoculated alone. This work thus reveals an additional important inflammasome activation mechanism by which oral keystone pathogens may stimulate periodontal disease progression.

This dataset

Open GSE339420 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 GSE339420_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 PRJNA1498632 and SRA study SRP720084. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly in duplicate

NLRP6-KO, Sg, biol ×3 WT, Sg, biol ×2 WT, Pg+Sg, biol ×2 WT, Sham, biol ×2 WT, Pg, biol ×2 WT, Negative, biol ×2 NLRP6-KO, Pg, biol ×2 NLRP6-KO, Pg+Sg, biol ×2 +1 more

Supports a between-group comparison across 17 samples.

How we read this: 8 replicated groups read from 18 sample titles; they account for 17 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

GSM9895647 WT, Sg, biol rep 1 WT, Sg, biol
GSM9895648 WT, Sg, biol rep 2 WT, Sg, biol
GSM9895649 WT, Pg+Sg, biol rep 1 WT, Pg+Sg, biol
GSM9895650 WT, Sham, biol rep 1 WT, Sham, biol
GSM9895651 WT, Pg, biol rep 1 WT, Pg, biol
GSM9895652 WT, Negative, biol rep 1 WT, Negative, biol
GSM9895653 WT, Sham, biol rep 2 WT, Sham, biol
GSM9895654 WT, Pg, biol rep 2 WT, Pg, biol
GSM9895655 WT, Negative, biol rep 2 WT, Negative, biol
GSM9895656 NLRP6-KO, Sg, biol rep 1 NLRP6-KO, Sg, biol
GSM9895657 NLRP6-KO, Sg, biol rep 2 NLRP6-KO, Sg, biol
GSM9895658 NLRP6-KO, Negative, biol rep 1
GSM9895659 NLRP6-KO, Pg, biol rep 1 NLRP6-KO, Pg, biol
GSM9895660 NLRP6-KO, Pg, biol rep 2 NLRP6-KO, Pg, biol
GSM9895661 NLRP6-KO, Pg+Sg, biol rep 1 NLRP6-KO, Pg+Sg, biol
GSM9895662 NLRP6-KO, Pg+Sg, biol rep 2 NLRP6-KO, Pg+Sg, biol
GSM9895663 NLRP6-KO, Sg, biol rep 3 NLRP6-KO, Sg, biol
GSM9895664 WT, Pg+Sg, biol rep 2 WT, Pg+Sg, biol

Datasets on a similar topic

GSE274669 Modulation of Integrin α9β1 in Macrophages Reduces Periodontal Inflammation and Supports Alveolar Bone Preservation in Periodontitis [RNA-seq] 12 samples shares periodontitis, alveolar, bone
GSE298066 Ligature-induced periodontitis (LIP) induces rapid alveolar bone loss followed by gingival immunosuppressive conditions 11 samples shares periodontitis, alveolar, bone
GSE274670 Modulation of Integrin α9β1 in Macrophages Reduces Periodontal Inflammation and Supports Alveolar Bone Preservation in Periodontitis [scRNA-seq] 4 samples shares periodontitis, alveolar, bone
GSE292710 Traumatic occlusion exacerbates bone resorption by modifying gene expression in the bone tissue of ligature-induced periodontitis in mice 32 samples shares periodontitis, bone
GSE327719 Estrogen deprivation alters gingival and dentoalveolar complex transcriptomes during ligature-induced periodontitis in mice 24 samples shares periodontitis, alveolar
GSE316444 Traumatic occlusion exacerbates bone resorption by modifying gene expression in the bone tissue of ligature-induced periodontitis in mice. 16 samples shares periodontitis, bone
GSE293227 Type I interferon protects against bone loss in periodontitis by mitigating an interleukin (IL)-17-neutrophil axis [RNA-Seq] 10 samples shares periodontitis, bone
GSE254766 The neutrophil–osteogenic cell axis promotes bone destruction in periodontitis 2 samples shares periodontitis, bone

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.