scRNA-seq of splenic CD45+ Cells from Aire-knockout rats
Data files
Apr 17, 2025 version files 119.72 MB
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AireKO_SPL.zip
119.72 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+ splenic cells from 7-month-old Aire-knockout rats (n=4) with high levels of anti-IFNα autoantibodies and age-matched Aire-heterozygous controls (n=4). Splenic cells were isolated through mechanical homogenization, followed by erythrocyte lysis and CD45+ cell sorting using a MA900 cell sorter. Single cells were captured with the 10x Chromium microfluidics system, and barcoded cDNA libraries were prepared using the single-cell 3’ mRNA kit (10x Genomics). Sequencing was conducted 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. 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
Overview
This dataset contains scRNA-seq data from Aire-deficient (KO) and Aire-sufficient (HE) animals, organized into separate folders for each sample. The data were collected to investigate immune cell populations and gene expression patterns in Aire-deficient and Aire-sufficient animals. 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 using the following format:
HE_<ID>: Sample collected from an Aire-sufficient (HE) animalKO_<ID>: Sample collected from an Aire-deficient (KO) animal
The <ID> number after the underscore 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.
CD45+ splenic cells were isolated from 7-month-old Aire-knockout rats (n=4) with high levels of anti-IFNα autoantibodies and age-matched Aire-heterozygous controls (n=4). Spleens were homogenized mechanically, and erythrocytes were removed using an ACK lysis solution. The CD45+ cell population was sorted using a MA900 cell sorter (Sony Biotechnology). Single-cell RNA sequencing (scRNA-seq) was performed with the 10x Chromium microfluidics system, and barcoded cDNA libraries were constructed using the single-cell 3’ mRNA kit (10x Genomics). Sequencing was conducted on the Illumina MiSeq platform. The data were processed using the Cell Ranger software suite (Version 6.0.1, 10x Genomics Inc.) and aligned to the Rattus norvegicus reference genome (Rnor_6.0).