Transcriptome Profiling of CD4+ T cell subpopulations from Aire-Knockout Rats
Data files
Apr 17, 2025 version files 71.52 MB
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AireKO_Tcell_bulk.zip
71.52 MB
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README.md
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Abstract
The dataset consists of microarray gene expression data from four key CD4+ T cell populations—Tconv, Treg, Tfh, and Tfr—isolated from 7-month-old Aire-knockout rats with high levels of anti-IFNα autoantibodies and age-matched control rats. The cells were isolated from spleens and axillary lymph nodes using flow cytometry, with each population being sorted based on specific markers (CD3+ CD4+ CD25- ICOS- for Tconv, CD25+ ICOS- for Treg, CD25- ICOS+ for Tfh, and CD25+ ICOS+ for Tfr). RNA was purified from these sorted populations, and transcriptome analysis was performed using Clariom™ S Pico Assay HT gene expression chips.
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.CEL files derived from transcriptome profiling of T cell populations isolated from Aire-deficient (KO) rats and control (HE) animals. The samples are sorted from various tissues, including spleens and lymph nodes. The dataset consists of sorted T cell populations including T conventional cells (Tconv), T regulatory cells (Treg), T follicular regulatory cells (Tfr), and T follicular helper cells (Tfh).
File Structure
The archive contains .CEL files named according to the following convention:
[well number][genotype] [animal ID][cell population and tissue].CEL
File Naming Legend
Each file name follows a standardized format. Here’s how to interpret each part:
- [well number]: The specific well identifier for the sample.
- [genotype]: Indicates whether the sample was collected from an Aire-deficient rat (KO) or a control rat (HE).
- [animal ID]: A unique identifier for the animal from which the sample was taken.
- [cell population]: Specifies the T cell population isolated from the sample. This can be one of the following:
- Tconv: T conventional cells
- Treg: T regulatory cells
- Tfr: T follicular regulatory cells
- Tfh: T follicular helper cells
- [tissue]: The tissue from which the sample was collected. This can be one of the following:
- SPL: Spleen
- LN: Lymph Node
CEL files can be opened using the Transcriptome Analysis Console (TAC) Software (ThermoFisher).
Spleens and axillary lymph nodes were homogenized to create a single-cell suspension. Erythrocytes were lysed from splenic samples using an ACK solution. For transcriptome analysis, T cell populations were sorted based on specific markers (CD3+ CD4+ CD25- ICOS- for Tconv, CD3+ CD4+ CD25+ ICOS- for Treg, CD3+ CD4+ CD25- ICOS+ for Tfh, and CD3+ CD4+ CD25+ ICOS+ for Tfr) using the MA900 cell sorter. RNA was purified from the sorted cells, with quality assessed by the Agilent RNA 6000 Pico kit, and samples with a RIN >7.5 were selected for analysis. Transcriptome profiling was performed using the Genetitan MC machine on Clariom™ S Pico Assay HT gene expression chips.