Spatially clustered type I interferon responses at injury borderzones [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: 10 distinct titles, 1 of them repeatedGroups 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
- Spatially clustered type I interferon responses at injury borderzonesNature · 2024
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 GSE268876_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 PRJNA1119369 and SRA study SRP511302. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 12 sample titles: 10 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.
- GSM8301921 IfnarKO_D4_WC1, biol rep1
- GSM8301922 IfnarKO_D4_WC2, biol rep2
- GSM8301923 WT_D4_WC1, biol rep1
- GSM8301924 WT_D4_WC2, biol rep2
- GSM8301925 WT_D4_WC3, biol rep3
- GSM8301926 WT_D4_WC4, biol rep4
- GSM8301927 Irf3KO_D3_nuclei1, biol rep1
- GSM8301928 Irf3KO_D3_nuclei2, biol rep2
- GSM8301929 Irf3KO_D3_nuclei3, biol rep3
- GSM8301930 WT_D3_nuclei1
- GSM8301931 WT_D3_nuclei2
- GSM8301932 WT_D3_nuclei3
- GSE289723 Interleukin-4 modulates type I interferon to augment anti-tumour immunity [scRNA-Seq] 36 samples shares interferon, scrna-seq, type
- GSE247149 Type III interferons induce pyroptosis in gut epithelial cells and delay tissue restitution upon acute intestinal injury. 16 samples shares interferon, injury, type
- GSE328709 Type I interferon signaling in microglia drives synaptic engulfment and neuronal loss following traumatic brain injury 13 samples shares interferon, injury, type
- GSE275283 Inhibition of tumor-intrinsic NAT10 enhances antitumor immunity by triggering type I interferon responses via MYC/CDK2/DNMT1 pathway 18 samples shares interferon, type
- GSE287098 Influenza virus-induced type I interferons disrupt alveolar epithelial repair and tight junction integrity in the developing lung 96 samples shares interferon, type
- GSE281234 TFEB and TFE3 regulate STING1-dependent immune responses by controlling type I interferon signaling [AM_NIH_RNASeq_50538] 12 samples shares interferon, type
- GSE304521 SEX-DEPENDENT TYPE I INTERFERON SIGNALING EXACERBATES ALZHEIMER'S PATHOLOGY 82 samples shares interferon, type
- GSE161562 Transcriptome alteration in Nrf2 mutant developing oligodendrocytes treated with interferon gamma and thapsigargin in comparison with wild-type developing oligodendrocytes treated with interferon gamma and thapsigargin 50 samples shares interferon, type
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.