DOI: 10.5061/dryad.mpg4f4r9z
title: Transcriptome Profiling of CD4+ T cell subpopulations from Aire-Knockout Rats

description: 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.
description: 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 &gt;7.5 were selected for analysis.
 Transcriptome profiling was performed using the Genetitan MC machine on
 Clariom™ S Pico Assay HT gene expression chips.
description: # README for Microarray Dataset of T Cell Subpopulations from
 Aire-Knockout 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* ## 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).