DOI: 10.5061/dryad.5qfttdzhj
title: scRNA-seq of CD45+ cells from salivary gland of Aire-knockout rats

description: 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.
description: 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.
description: # README for scRNA-seq Dataset of CD45+ Cells from Salivary Gland of
 Aire-Deficient Rat ## 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* ## 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.