Age-related epithelial defects limit thymic function and regeneration [single cell]
Single-cell RNA-seq · mouse · 29 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
- 29 samples: 29 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
- Age-related epithelial defects limit thymic function and regenerationNature 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 GSE240016_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 PRJNA1001924 and SRA study SRP453223. 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 29 sample titles: 29 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.
- GSM7679869 02-mo CD45- thymic stoma cells - steady state rep1 [singe cell]
- GSM7679870 02-mo CD45- thymic stoma cells - steady state rep2 [singe cell]
- GSM7679871 02-mo CD45- thymic endothelial cells - steady state [singe cell]
- GSM7679872 02-mo CD45- thymic fibroblasts - steady state [singe cell]
- GSM7679873 02-mo CD45- thymic stoma cells - day 1 after SL-TBI rep1 [singe cell]
- GSM7679874 02-mo CD45- thymic stoma cells - day 1 after SL-TBI rep2 [singe cell]
- GSM7679875 02-mo CD45- thymic endothelial cells - day 1 after SL-TBI [singe cell]
- GSM7679876 02-mo CD45- thymic fibroblasts - day 1 after SL-TBI [singe cell]
- GSM7679877 02-mo CD45- thymic stoma cells - day 4 after SL-TBI rep1 [singe cell]
- GSM7679878 02-mo CD45- thymic stoma cells - day 4 after SL-TBI rep2 [singe cell]
- GSM7679879 02-mo CD45- thymic endothelial cells - day 4 after SL-TBI [singe cell]
- GSM7679880 02-mo CD45- thymic fibroblasts - day 4 after SL-TBI [singe cell]
- GSM7679881 02-mo CD45- thymic stoma cells - day 7 after SL-TBI rep1 [singe cell]
- GSM7679882 02-mo CD45- thymic stoma cells - day 7 after SL-TBI rep2 [singe cell]
- GSM7679883 02-mo CD45- thymic endothelial cells - day 7 after SL-TBI [singe cell]
- GSM7679884 02-mo CD45- thymic fibroblasts - day 7 after SL-TBI [singe cell]
- GSM7679885 18-mo CD45- thymic stoma cells - steady state rep1 [singe cell]
- GSM7679886 18-mo CD45- thymic stoma cells - steady state rep2 [singe cell]
- GSM7679887 18-mo CD45- thymic endothelial cells - steady state [singe cell]
- GSM7679888 18-mo CD45- thymic fibroblasts - steady state [singe cell]
- GSM7679889 18-mo CD45- thymic stoma cells - day 1 after SL-TBI [singe cell]
- GSM7679890 18-mo CD45- thymic endothelial cells - day 1 after SL-TBI [singe cell]
- GSM7679891 18-mo CD45- thymic fibroblasts - day 1 after SL-TBI [singe cell]
- GSM7679892 18-mo CD45- thymic stoma cells - day 4 after SL-TBI [singe cell]
- GSM7679893 18-mo CD45- thymic endothelial cells - day 4 after SL-TBI [singe cell]
- GSM7679894 18-mo CD45- thymic fibroblasts - day 4 after SL-TBI [singe cell]
- GSM7679895 18-mo CD45- thymic stoma cells - day 7 after SL-TBI [singe cell]
- GSM7679896 18-mo CD45- thymic endothelial cells - day 7 after SL-TBI [singe cell]
- GSM7679897 18-mo CD45- thymic fibroblasts - day 7 after SL-TBI [singe cell]
- GSE249753 Age-related epithelial defects limit thymic function and regeneration [single cell; Foxn1Lin] 3 samples shares regeneration, age-related, epithelial, defects, thymic, limit
- GSE240020 Age-related epithelial defects limit thymic function and regeneration 51 samples shares regeneration, age-related, epithelial, defects, thymic, limit
- GSE205410 Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [bulkRNA-seq] 47 samples shares epithelial, thymic
- GSE220665 The Transcriptional Cofactor SKI Regulates Medullary Thymic Epithelial Cell Differentiation and Peripheral T Cell Responses 42 samples shares epithelial, thymic
- GSE240698 Thymic epithelial organoids mediate T cell development 11 samples shares epithelial, thymic
- GSE326641 Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [scRNA-seq] 8 samples shares regeneration, epithelial
- GSE267938 Functional optic tract rewiring via subtype- and target-specific axonal regeneration and presynaptic activity enhancement 256 samples shares regeneration
- GSE267936 Functional Optic Tract Rewiring via Subtype- and Target-specific Axonal Regeneration and Presynaptic Activity Enhancement (bulk RNA-Seq) 40 samples shares regeneration
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.