scRNA-seq of thymic epithelial cells from Aire-knockout rats
Data files
Apr 17, 2025 version files 372.50 MB
-
AireKO_TEC.zip
372.50 MB
-
README.md
1.85 KB
Abstract
This dataset investigates the impact of Aire deficiency on thymic stromal cell subpopulations in rats using single-cell RNA sequencing (scRNA-seq). CD45-, EpCAM+ thymic epithelial cells (TECs) were isolated from the thymi of 6-week-old Aire-knockout (n=4) and Aire-heterozygous control (n=3) rats via flow cytometry. The cells underwent enzymatic digestion to enrich the stromal compartment, and single cells were processed using the 10x Chromium platform with barcoded cDNA libraries prepared using the single-cell 3’ mRNA kit. Sequencing was performed on the Illumina MiSeq platform, and gene expression data were mapped to the Rattus norvegicus reference genome (Rnor_6.0) using Cell Ranger (v6.0.1). The dataset includes processed count matrices generated by Cell Ranger.
Related Datasets
This dataset is part of a coordinated set of transcriptomic and single-cell transcriptomic profiles generated from Aire-knockout rats for the associated research article. Additional related datasets can be accessed via Dryad at the following DOIs:
- 10.5061/dryad.mpg4f4r9z: Transcriptome Profiling of CD4+ T cell subpopulations
- 10.5061/dryad.p8cz8wb1s: Transcriptome Profiling of Medullary Thymic Epithelial Cells
- 10.5061/dryad.8kprr4xz1: scRNA-seq of Thymic Epithelial Cells
- 10.5061/dryad.hhmgqnksj: scRNA-seq of Splenic CD45+ Cells
- 10.5061/dryad.5qfttdzhj: scRNA-seq of CD45+ Cells from Salivary Gland
Overview
This dataset contains single-cell RNA sequencing (scRNA-seq) data from thymic stromal cells of Aire-sufficient (HE) and Aire-deficient (KO) rats. The data is organized into 7 folders, with folder names indicating whether the sample was collected from an Aire-sufficient (HE) or Aire-deficient (KO) animal.
Folder Structure
- Each folder represents a biological replicate.
- Folder naming convention:
T_[HE|KO], where:HE: Aire-sufficient sampleKO: Aire-deficient sample
Contents of Each Folder
Each folder includes the following files:
barcodes.tsv.gz: Contains barcodes for individual cells in the sample.features.tsv.gz: Lists detected genes or features in the dataset.matrix.mtx.gz: Sparse matrix containing raw gene expression counts.
Data Format
- The files are compressed (
.gz) and need to be extracted before use.
Thymi from 6-week-old Aire-knockout and Aire-heterozygous control rats were minced and gravity-sedimented to isolate stromal cells and thymocytes. Stromal cells were enriched through enzymatic digestion using collagenase, DNase, and dispase, and sorted into the CD45-, EpCAM+ population using flow cytometry. Single cells were captured with the 10x Chromium microfluidics system, and barcoded cDNA libraries were prepared using the 10x Genomics single-cell 3’ mRNA kit. Libraries were sequenced on the Illumina MiSeq platform, and the data were mapped to the Rattus norvegicus reference genome (Rnor_6.0) and quantified using the Cell Ranger software suite (v6.0.1).