Chikungunya virus persists in joint-associated macrophages and promotes chronic disease in mice [scRNA-seq]
Single-cell RNA-seq · mouse · 12 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples: 3 × M vs 3 × A vs 3 × U vs 3 × CGroups 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
- Chikungunya virus persists in joint-associated macrophages and promotes chronic disease in miceNature microbiology · 2026
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 GSE300299_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1280064 and SRA study SRP593423. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
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.
- GSM9057971 M1 M
- GSM9057972 M2 M
- GSM9057973 M3 M
- GSM9057974 A1 A
- GSM9057975 A2 A
- GSM9057976 A3 A
- GSM9057977 U1 U
- GSM9057978 U2 U
- GSM9057979 U3 U
- GSM9057980 C1 C
- GSM9057981 C2 C
- GSM9057982 C3 C
- GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares macrophages, promotes
- GSE239287 Single-cell transcriptome sequencing of macrophages in acute kidney injury(AKI) to chronic kidney dieases(CKD) 17 samples shares macrophages, chronic
- GSE290194 Repair-Associated Macrophages Increase after Early-phase Microglia Attenuation to Promote Ischemic Stroke Recovery [scRNA-Seq] 16 samples shares macrophages, scrna-seq
- GSE272424 Rejuvenating endogenous antitumor immunity via a chimeric receptor-engineered oncolytic virus targeting tumor-associated macrophages 6 samples shares macrophages, virus
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares scrna-seq
- GSE271100 Stem cells tightly regulate dead cell clearance to maintain tissue fitness [scRNA-seq] 1037 samples shares scrna-seq
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares scrna-seq
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares macrophages
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.