AIRE drives early life thymic interferons and changes thymic self-antigen expression [bulk RNA-seq]
Single-cell RNA-seq · mouse · 75 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 75 samples: 17 conditions, mostly with about 4 replicates eachGroups 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
- Sterile production of interferons in the thymus affects T cell repertoire selectionScience immunology · 2024
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 GSE192715_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 PRJNA792824 and SRA study SRP352743. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 75 samples.
How we read this: 17 replicated groups read from 75 sample titles; they account for 75 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.
- GSM5761595 SIRPa IFNARKO 1 SIRPa IFNARKO
- GSM5761596 SIRPa IFNARKO 2 SIRPa IFNARKO
- GSM5761597 SIRPa IFNARKO 3 SIRPa IFNARKO
- GSM5761598 SIRPa IFNARKO 4 SIRPa IFNARKO
- GSM5761599 XCR1 IFNARKO 1 XCR1 IFNARKO
- GSM5761600 XCR1 IFNARKO 2 XCR1 IFNARKO
- GSM5761601 XCR1 IFNARKO 4 XCR1 IFNARKO
- GSM5761602 SIRPa IFNBKO 1 SIRPa IFNBKO
- GSM5761603 SIRPa IFNBKO 2 SIRPa IFNBKO
- GSM5761604 SIRPa IFNBKO 3 SIRPa IFNBKO
- GSM5761605 SIRPa IFNBKO 4 SIRPa IFNBKO
- GSM5761606 XCR1 IFNBKO 1 XCR1 IFNBKO
- GSM5761607 XCR1 IFNBKO 2 XCR1 IFNBKO
- GSM5761608 XCR1 IFNBKO 4 XCR1 IFNBKO
- GSM5761609 SIRPa DRKO 1 SIRPa DRKO
- GSM5761610 SIRPa DRKO 2 SIRPa DRKO
- GSM5761611 SIRPa DRKO 3 SIRPa DRKO
- GSM5761612 SIRPa DRKO 4 SIRPa DRKO
- GSM5761613 XCR1 DRKO 1 XCR1 DRKO
- GSM5761614 XCR1 DRKO 2 XCR1 DRKO
- GSM5761615 XCR1 DRKO 3 XCR1 DRKO
- GSM5761616 XCR1 DRKO 4 XCR1 DRKO
- GSM5761617 SIRPa STAT1KO 1 SIRPa STAT1KO
- GSM5761618 SIRPa STAT1KO 2 SIRPa STAT1KO
- GSM5761619 SIRPa STAT1KO 3 SIRPa STAT1KO
- GSM5761620 SIRPa STAT1KO 4 SIRPa STAT1KO
- GSM5761621 XCR1 STAT1KO 1 XCR1 STAT1KO
- GSM5761622 XCR1 STAT1KO 3 XCR1 STAT1KO
- GSM5761623 XCR1 STAT1KO 4 XCR1 STAT1KO
- GSM5761624 SIRPa WT 1 SIRPa WT
- GSM5761625 SIRPa WT 2 SIRPa WT
- GSM5761626 SIRPa WT 3 SIRPa WT
- GSM5761627 SIRPa WT 4 SIRPa WT
- GSM5761628 XCR1 WT 1 XCR1 WT
- GSM5761629 XCR1 WT 2 XCR1 WT
- GSM5761630 XCR1 WT 3 XCR1 WT
- GSM5761631 XCR1 WT 4 XCR1 WT
- GSM5761632 SIRPa IFNLR 1 SIRPa IFNL
- GSM5761633 SIRPa IFNLR 2 SIRPa IFNL
- GSM5761634 SIRPa IFNLR 3 SIRPa IFNL
+ 35 more — browse all 75 samples with per-sample file links →
- GSE205410 Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [bulkRNA-seq] 47 samples shares aire, rna-seq, thymic
- GSE226938 Early amyloid-induced changes in microglia gene expression in APP/PS1 mice [scRNA-seq] 36 samples shares changes, rna-seq, early
- GSE326648 Sexual dimorphism shapes AAK trajectory in Pax6 deficiency mouse model with early immune activation, impaired innervation, and altered tears 40 samples shares aire, early
- GSE276253 RNA-seq analysis of the brain of mice following recombinant HSV-1 carrying the S302A mutation in vUNG and the repaired HSV-1 strain 14 samples shares aire, rna-seq
- GSE267192 PPARγ-dependent Remodeling of Translational Machinery in Adipose Progenitors is Impaired in Obesity [scRNA-seq] 12 samples shares aire, rna-seq
- GSE265909 yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution. [scRNA-Seq] 563 samples shares changes, rna-seq
- GSE282096 Diminished transcriptional activity and splicing changes drive gene length-biased rewiring in the aging transcriptome (RNA-Seq) 94 samples shares changes, rna-seq
- GSE245251 Synaptic Activity Causes Minute-scale Changes in BAF Complex Composition and Function [RNA-Seq] 24 samples shares changes, 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.