DOI: 10.5061/dryad.8kprr4xz1
title: scRNA-seq of thymic epithelial cells from Aire-knockout rats

description: 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.
description: 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).
description: # README for scRNA-seq Dataset of Thymic Stromal Cells from Aire-Deficient
 Rats ## 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](https://doi.org/10.5061/dryad.mpg4f4r9z):
 *Transcriptome Profiling of CD4+ T cell subpopulations* *
 [10.5061/dryad.p8cz8wb1s](https://doi.org/10.5061/dryad.p8cz8wb1s):
 *Transcriptome Profiling of Medullary Thymic Epithelial Cells* *
 [10.5061/dryad.8kprr4xz1](https://doi.org/10.5061/dryad.8kprr4xz1):
 *scRNA-seq of Thymic Epithelial Cells* *
 [10.5061/dryad.hhmgqnksj](https://doi.org/10.5061/dryad.hhmgqnksj):
 *scRNA-seq of Splenic CD45+ Cells* *
 [10.5061/dryad.5qfttdzhj](https://doi.org/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 sample * `KO`: Aire-deficient sample ### Contents of Each
 Folder Each folder includes the following files: 1. **`barcodes.tsv.gz`**:
 Contains barcodes for individual cells in the sample. 2.
 **`features.tsv.gz`**: Lists detected genes or features in the dataset. 3.
 **`matrix.mtx.gz`**: Sparse matrix containing raw gene expression counts.
 ## Data Format * The files are compressed (`.gz`) and need to be extracted
 before use.