scRNA-seq of CD45+ cells from salivary gland of Aire-knockout rats
Data files
Apr 17, 2025 version files 129.27 MB
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AireKO_SG.zip
129.27 MB
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README.md
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Abstract
This dataset examines the impact of anti-IFNα autoantibodies on immune cell populations and gene expression in peripheral immune tissues of Aire-knockout rats. Single-cell RNA sequencing (scRNA-seq) was performed on CD45+ cells sorted from the submandibular salivary glands of seven-month-old Aire-deficient rats (n=4) and age-matched Aire-heterozygous control rats (n=3). The salivary glands were minced, enzymatically digested, and processed to avoid cell aggregation before sorting for CD45+ cells. The single cells were captured using the 10x Chromium platform, with cDNA libraries prepared using the single-cell 3’ mRNA kit. Sequencing was conducted on the Illumina MiSeq platform, and the data were mapped to the Rattus norvegicus reference genome (Rnor_6.0) and processed with the Cell Ranger software suite. The dataset includes 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
Dataset Overview
This dataset contains single-cell RNA-sequencing (scRNA-seq) data from immune cells sorted from the submandibular salivary glands of seven-month-old Aire-deficient rats (KO) and Aire-heterozygous control rats (HE). The data were collected to investigate the effect of anti-IFNα antibodies on immune cell populations infiltrating salivary glands of Aire KO rats. Each folder corresponds to a specific sample, with naming conventions that indicate whether the sample was collected from an Aire-deficient (KO) or sufficient (HE) animal.
Folder Structure
The dataset archive contains 8 folders, each named according to the following format:
HE_[0-9*]: Represents a sample collected from an Aire-sufficient (HE) animal.KO_[0-9*]: Represents a sample collected from an Aire-deficient (KO) animal.
The number following the prefix (HE or KO) uniquely identifies each sample.
Contents of Each Folder
Each folder contains the following files related to the single-cell RNA sequencing data:
barcodes.tsv.gz: Barcode information for each cell in the sample.features.tsv.gz: Information about the features (genes) detected in the sample.matrix.mtx.gz: The matrix file containing the gene expression counts for each cell.
Data Format
- The files are compressed (
.gz) and need to be extracted before use.
This dataset was collected by isolating CD45+ immune cells from the submandibular salivary glands of seven-month-old Aire-deficient rats (n=4) and age-matched Aire-heterozygous control rats (n=3). The salivary glands were minced and enzymatically digested using a combination of collagenase 4, DNase1, and Dispase to generate a single-cell suspension. The samples were processed to prevent aggregation and then sorted for CD45+ cells using an MA900 cell sorter. Single cells were captured using the 10x Chromium microfluidics platform, and barcoded cDNA libraries were prepared using the 10x Genomics single-cell 3’ mRNA kit. Sequencing was performed on the Illumina MiSeq platform, and the data were mapped to the Rattus norvegicus reference genome (Rnor_6.0) using the Cell Ranger software suite.