DOI: 10.5061/dryad.p8cz8wb1s
title: Transcriptome profiling of medullary thymic epithelial cells from Aire-knockout rats

description: This dataset contains transcriptome profiling data of thymic stromal cells
 from Aire-deficient and control rats. The thymic stromal cells were sorted
 into three fractions based on the expression of EpCAM, CD45, UEA1, and MHC
 markers: cTEC (Epcam+ CD45- UEA1low MHClo), mTEClo (Epcam+ CD45- UEA1med
 MHCmed), and mTEChi (Epcam+ CD45- UEA1high MHChi). RNA was extracted from
 these sorted cells, and RNA quality was assessed, with samples having a
 RIN &gt;7.5 used for further analysis. The transcriptome analysis was
 performed using an Affymetrix GeneTitan MC system and Clariom™ S Pico
 Assay HT chip. The data for the mTEChi fraction are provided as .CEL
 files, which can be used for downstream gene expression analysis.
description: The thymi were minced, gravity-sedimented, and enzymatically
 digested to enrich for stromal cells. These cells were then sorted into
 three populations—cTEC, mTEClo, and mTEChi—based on the expression of
 specific markers (EpCAM, CD45, UEA1, and MHC). RNA was extracted from the
 sorted cells using the RNeasy Micro kit, and RNA quality was assessed
 using the Agilent RNA 6000 Pico kit. Only samples with a RIN &gt;7.5
 were used for transcriptome analysis. Gene expression profiling was
 performed using the Affymetrix GeneTitan MC system and Clariom™ S Pico
 Assay HT chip, and the resulting data for the mTEChi population are
 provided as .CEL files for further analysis.
description: # README for Microarray Dataset of Medullary Thymic Epithelial Cells 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 gene expression data from thymic stromal cells sorted
 from Aire-deficient (KO) and control (HE) rats. The data is organized into
 six files, each representing a distinct biological replicate of the mTEChi
 population. ## File Naming Convention * **Genotype**: Specifies whether
 the sample was collected from an Aire-deficient (KO) rat or a control (HE)
 rat. * `KO`: Aire-deficient rat (Aire-knockout) * `HE`: Control
 (Aire-sufficient) rat * **Sample Identifier**: A unique identifier for
 each biological replicate, denoted by a specific sample name or number
 (e.g., P20-3). CEL files can be opened using the Transcriptome Analysis
 Console (TAC) Software (ThermoFisher).