Bulk RNA-seq of wild-type and Nlrp3-/- bone marrow-derived macrophages with or without LPS and ATP costimulation
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: 12 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
- The P2X7R/NLRP3 inflammasome axis suppresses enthesis regeneration through inflammatory and metabolic macrophage-stem cell cross-talkScience advances · 2025
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 GSE286554_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 PRJNA1209897 and SRA study SRP556965. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 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.
- GSM8729196 wild type BMDM with costimulation, replicate 1, RNA-seq
- GSM8729197 wild type BMDM with costimulation, replicate 2, RNA-seq
- GSM8729198 wild type BMDM with costimulation, replicate 3, RNA-seq
- GSM8729199 wild type BMDM without costimulation, replicate 1, RNA-seq
- GSM8729200 wild type BMDM without costimulation, replicate 2, RNA-seq
- GSM8729201 wild type BMDM without costimulation, replicate 3, RNA-seq
- GSM8729202 Nlrp3-/- BMDM with costimulation, replicate 1, RNA-seq
- GSM8729203 Nlrp3-/- BMDM with costimulation, replicate 2, RNA-seq
- GSM8729204 Nlrp3-/- BMDM with costimulation, replicate 3, RNA-seq
- GSM8729205 Nlrp3-/- BMDM without costimulation, replicate 1, RNA-seq
- GSM8729206 Nlrp3-/- BMDM without costimulation, replicate 2, RNA-seq
- GSM8729207 Nlrp3-/- BMDM without costimulation, replicate 3, RNA-seq
- GSE235016 RNA-seq revealed the anti-pyroptotic effect of suramin by suppressing NLRP3/caspase-1/GSDMD pathway in LPS-induced MH-S alveolar macrophages 9 samples shares nlrp3, lps, macrophages, rna-seq
- GSE269886 Transcriptomic analysis of microglia from young and aged wild-type, NLRP3-/-, APP/PS1 and APP/PS1.NLRP3-/- mice. 62 samples shares nlrp3, wild-type
- GSE231931 RNA-seq analysis of B cells cultured with LPS and IL-12 and/or IFN gamma 42 samples shares lps, rna-seq
- GSE201128 The response to lipopolysaccharide (LPS) of bone marrow derived macrophages treated with oxysterol binding protein (OSBP) inhibitors 30 samples shares lps, macrophages
- GSE264280 Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2 (RNA-seq) 30 samples shares atp, rna-seq
- GSE264278 TIme-cource single-cell RNA-seq analysis of bleomycin and LPS-induced lung injury and fibrosis 18 samples shares lps, rna-seq
- GSE268843 Gene expression analysis of macrophages exposed to LPS and LPS-coated beads 18 samples shares lps, macrophages
- GSE268405 LPS-induced TIR domain complex acetylation activated TLR4/MAL/MyD88 signal pathway in sepsis [RNA-Seq] 18 samples shares lps, rna-seq
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.