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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 10, 2020 |
| Title |
RNA microarray of sorted dendritic epidermal T cells of aryl hydrocarbon receptor deficient mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
To assess the role of the aryl hydrocarbon receptor (AHR) receptor in dendritic epidermal T cells (DETC), we sorted DETC from 2 weeks old mice homozygous and heterozygous for AHR-knockout. While DETC are not maintained in the epidermis of mice with a homozygous AHR-knockout, those in heterozygous mice devellop normally. The age at 2 weeks is critical for the DETC establishment and the peak time of the so-called proliferation burst of DETC in wildtype mice. DETC were identified in epidermal cell suspension by expression of the gamma-delta T cell receptor. The DETC proportion of live epidermal cells was between 10-15 % in Ahr-het and 2-4 % in Ahr-ko mice. After FACS-sorting to a purity of 90-98 %, DETC were lysed and their RNA was extracted. Three RNA samples for each genotype were generated, by pooling the RNA of 2-3 mice for each sample. RNA was processed and hybridized to Applied BiosystemsTM ClariomTM S Mouse Gene Expression Microarrays. Using the Software package R the data were normalized using the Robust Multichip Average algorithm (RMA) and significance of differentially regulated genes was assessed by the False Discovery Rate (FDR) using the Benjamini and Hochberg’s method.
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| Overall design |
We performed RNA-microarrays to assess the role of the aryl hydrocarbon receptor (AHR) receptor in dendritic epidermal T cells (DETC). Therefore, we sorted DETC from 2 weeks old mice homozygous and heterozygous for AHR-knockout. The DETC proportion of live epidermal cells was between 10-15 % in Ahr-het and 2-4 % in Ahr-ko mice. DETC were identified in epidermal cell suspension by expression of the gamma-delta T cell receptor, FACS-sorted to a purity of 90-98 %, lysed and their RNA was extracted. Three RNA samples for each genotype were generated, by pooling the RNA of 2-3 mice for each sample. Three RNA samples for each genotype were generated, by pooling the RNA of 2-3 mice for each sample. RNA was processed and hybridized to Applied BiosystemsTM ClariomTM S Mouse Gene Expression Microarrays. The data were normalized using the Robust Multichip Average algorithm (RMA) and significance of differentially regulated genes was assessed by the False Discovery Rate (FDR) using the Benjamini and Hochberg’s method.
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| Contributor(s) |
Merches K, Schiavi A, Teichweyde N, Petzsch P, Köhrer K, Esser C |
| Citation(s) |
32256272, 32213963 |
| Submission date |
Dec 20, 2019 |
| Last update date |
Apr 13, 2020 |
| Contact name |
Katja Merches |
| Organization name |
Leibniz Institute for Environmental Medicine
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| Street address |
Auf'm Hennekamp 50
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| City |
Düsseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
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| Platforms (1) |
| GPL23038 |
[Clariom_S_Mouse] Affymetrix Clariom S Assay, Mouse (Includes Pico Assay) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA597025 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE142437_26_07_2019_DeG_without_statistical_filter_annotated.xlsx |
3.4 Mb |
(ftp)(http) |
XLSX |
| GSE142437_RAW.tar |
7.4 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
| Processed data are available on Series record |
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