IRF5 produced by kidney macrophages promotes polycystic kidney disease
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.
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 GSE127881_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 PRJNA525686 and SRA study SRP187585. 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.
- GSM3640468 2K: 1745__11220_S7
- GSM3640469 2K: 1746__11233_S8
- GSM3640470 2K: 1747__11226_S9
- GSM3640471 2K: 1755__2K-creplus_S1
- GSM3640472 2K: 1744__11230_S6
- GSM3640473 2K: 1748__11227_S10
- GSM3640474 1K: 1753__11225_S15
- GSM3640475 1K: 1751__11223_S13
- GSM3640476 1K: 1752__11224_S14
- GSM3640477 1K: 1750__11222_S12
- GSM3640478 1K: 1749__11221_S11
- GSM3640479 1K: 1754__11231_S16
- GSE300299 Chikungunya virus persists in joint-associated macrophages and promotes chronic disease in mice [scRNA-seq] 12 samples shares macrophages, promotes
- GSE300925 Lyn expression in macrophages promotes TLR activation and restricts proliferation in an isoform-independent manner 48 samples shares macrophages, promotes
- GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares macrophages, promotes
- GSE244450 Unraveling Epigenetic and Immune Mechanisms Underlying Cystogenesis in Autosomal Dominant Polycystic Kidney Disease 19 samples shares polycystic, kidney
- GSE239287 Single-cell transcriptome sequencing of macrophages in acute kidney injury(AKI) to chronic kidney dieases(CKD) 17 samples shares macrophages, kidney
- GSE284505 Chronic sleep deprivation promotes experimental autoimmune uveitis through STAT1 phosphorylation, ISG15 expression and enhanced pathogenicity of macrophages 12 samples shares macrophages, promotes
- GSE319035 P21+TREM2+-Senescent Macrophages Fuel Inflammaging and Metabolic Dysfunction-Associated Steatotic Liver Disease [NAFLD_time_course] 77 samples shares macrophages
- GSE285614 Adipocyte death drives fat redistribution from adipocytes to hepatocytes in steatotic liver disease via S100A8+ macrophages [RNA-seq] 34 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.