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Series GSE44945 Query DataSets for GSE44945
Status Public on May 07, 2013
Title Transcriptome sequencing of neonatal thymic epithelial cells.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: In all vertebrates, the thymus is necessary and sufficient for production of classic adaptive T cells. The key components of the thymus are cortical and medullary thymic epithelial cells (cTECs and mTECs). Despite the capital role of TECs, our understanding of TEC biology is quite rudimentary. For instance, we ignore what might be the extent of divergence in the functional program of these two TECs populations. It also remains unclear why the number of TECs decreases rapidly with age, thereby leading to progressive thymic insufficiency.
Methods: Systems level understanding of cell function begins with gene expression profiling, and the transcriptome is currently the only '-ome' that can be reliably tackled in its entirety in freshly harvested primary cells. In order to gain novel insights into TEC biology, we therefore decided to analyse the whole transcriptome of cTECs, mTECs and skin epithelial cells. We elected to analyse gene expression using RNA-seq rather microarrays because RNA-seq has higher sensitivity and dynamic range coupled to lower technical variations.
Results: Our deep sequencing approach provides a unique perspective into the transcriptome of TECs. Consistent with their ability to express ectopic genes, we found that mTECs expressed more genes than other cell populations. Out of a total of 15,069 genes expressed in TECs, 25% were differentially expressed by at least 5-fold in cTECs vs. mTECs. Genes expressed at higher levels in cTECs than mTECs regulate numerous cell functions including cell differentiation, cell movement and microtubule dynamics. Almost all positive regulators of the cell cycle were overexpressed in skin ECs relative to TECs.
Conclusions: Our RNA-seq data provide novel insights into the transcriptional landscape of TECs, highlight substantial divergences in the transcriptome of TEC subsets and suggest that cell cycle progression is differentially regulated in TECS and skinECs. We believe that our work will therefore represent a valuable resource and will be of great interest to readers working in biological sciences, particularly in the areas of immunology and systems biology.
Overall design The mRNA profiles of cTEC, mTEC (from 14 thymi of 7-days old C57BL/6 mice) and skinEC (from the trunk and dorsum of seven newborn mice) were generated by RNA-sequencing using Illumina HiSeq2000.
Contributor(s) St-Pierre C, Brochu S, Perreault C
Citation(s) 23681267
Submission date Mar 07, 2013
Last update date May 15, 2019
Contact name Charles St-Pierre
Organization name Montreal University
Department Institute for Research in Immunology and Cancer
Lab Immunobiology - Claude Perreault
Street address 2950, Chemin de Polytechnique
City Montreal
State/province Quebec
ZIP/Postal code H3T 1J4
Country Canada
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (3)
GSM1094283 cTEC
GSM1094284 mTEC
GSM1094285 skinEC
BioProject PRJNA192590
SRA SRP019027

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE44945_processed_data_file.xls.gz 8.4 Mb (ftp)(http) XLS
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Processed data are available on Series record
Raw data are available in SRA

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