Project description:In this study, we used the murine (Mus musculus) medullary thymic epithelial cell line (mTEC 3.10 cell line) co-cultured with fresh thymocytes as a functional assay for mTEC-thymocyte adhesion. Then we analyzed the differential transcriptional profile of this cell line, by means of Agilent oligo microarray hybridization, comparing Autoimmune regulator (Aire) wild-type cells vs Crispr-Cas9-induced Aire KO cells. The comparative transcriptional expression signatures allowed us to find those differentially expressed mRNAs or lncRNAs between the samples tested.

2021-12-31 | E-MTAB-6541 | biostudies-arrayexpress

Sequencing of Mus musculus muscle after physical exercise in C57BL/6 and NRF2-KO

Project description:Comparison of gene expression profiles from Mus musculus muscle after physical exercise (treadmill). The RNA-seq data comprise 4 groups: 2 strains, each w/ and w/o physical exercise. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

2021-10-19 | GSE110850 | GEO

The effect of Dicer knockdown on the microRNA transcriptional profile of 3.10 mTEC cell line.

Project description:Dicer, also known as endoribonuclease Dicer or helicase with RNase motif, cleaves double-stranded RNA (dsRNA) and pre-microRNA (pre-miRNA) into short mature double-stranded RNA fragments called small interfering RNA and microRNA, respectively. MicroRNAs are potent post-transcriptional regulators in developmental switches, lineage commitment and gene expression regulation. To evaluate their post-transcriptional role in gene expression of Medullary thymic epithelial cells (mTECS) we knocked down Dicer transcript by means of siRNA transfection in a Mus musculus mTEC cell line (3.10 mTEC). The Agilent oligo microarrays were used to determine the large scale microRNA (miRNA) transcriptional profiles of control or Dicer-knockdown 3.10 mTECs.

2016-06-27 | E-MTAB-4627 | biostudies-arrayexpress

The effect of the autoimmune regulator (Aire) gene on the transcriptional expression profile of 3.10 mTEC cell line.

Project description:Medullary thymic epithelial cells (mTECs) contribute to self-tolerance through the ectopic expression of peripheral tissue antigens (PTAs) in the thymus. PTA expression in mTECs is largely dependent on the autoimmune regulator (Aire) gene. Here we used a Mus musculus mTEC cell line (3.10 mTEC line, which constitutively express Aire in culture) to knockdown Aire gene by means of siRNA transfection. Aire knockdown was confirmed by means of qRT-PCR and RNA-FISH (for Aire mRNA levels), immunofluorescence and western blot (for AIRE protein levels).The Agilent oligo microarrays were used to determine the large scale transcriptional expression profiles of control or Aire-knockdown 3.10 mTECs.

2015-12-31 | E-MTAB-3879 | biostudies-arrayexpress

Crispr-Cas9-mediated Aire gene editing in medullary thymic epithelial (mTEC) cells shows its role as a gene expression modulator during thymocyte adhesion

Project description:The aim of this study is to evaluate the effect of Autoimmune regulator (Aire) gene disruption in a murine medullary thymic epithelial cells (mTEC 3.10 cell line) on the transcriptome of these cells during its adhesion with thymocytes. The mTEC-thymocyte adhesion is a crucial step for the negative selection of autoreactive thymocytes and prevention of autoimmune diseases. To generate Aire mutant cell clones, a total of 5x10^5 mTEC 3.10 cells were electro-transfected (Lonza Nucleofector) with CRISPR-Cas9 plasmid targeting the Aire Exon 3 (plasmid "all in one" encoding Aire Exon 3 gRNA + Cas9 + GFP, from Sigma-Aldrich). The GFP positive mTEC single cells were sorted by using a FACS Aria III cytometer and cells were cloned by expansion in culture. Sanger sequencing of PCR products from the Aire Exon 3 of these clones was used in order to evaluate the occurrence of indel mutations within the targeted Exon 3. The mTEC 3.10 clone E6 was identified and validated as a compound heterozygous Aire KO (Aire +/-). This clone features the Aire allele 1 that encodes a mutant Aire protein carring a neutral aminoacid substitution (A118P) and allele 2 encoding a truncated Aire protein. Wild type (WT) mTEC 3.10 cells or mTEC 3.10 clone E6 were cultured in the presence (or not) of thymocytes in order to establish cell adhesion. The total RNA preparations from WT or clone E6 mTEC cells (before or after mTEC- thymocyte co-cultures) were then sequenced through RNA-sequencing using a Illumina HiSeq 2500 instrument and the TruSeq Stranded mRNA Library Preparation kit resulting in about 50 million paired-end stranded specific 100 bp reads per sample. Sequencing reads were mapped to Mus musculus reference genome (mm10) using STAR v.2.5.0a. Read counts over transcripts were calculated using HTSeq v.0.6.1p2 based on a current UCSC annotation file for GRCm38/mm10 (Dec. 2011).

2018-06-15 | GSE91015 | GEO

Mus musculus 22k comparison of samples

Project description:Comparision of Mus musculus Control and Treated samples.

2009-01-01 | GSE13082 | GEO