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Genome-wide gene expression profiling of homeodomain-interacting protein kinase 2 deficient medullary thymic epithelial cells.

Rattay K, Derbinski J, Hofmann TG, Kyewski B - Genom Data (2015)

Bottom Line: Yet the full composition of this Aire-associated multi-protein complex and its mode of action remain to be elucidated.The changes in gene expression are presumably mediated through a regulatory effect of Hipk2 on AIRE as published in the study by Rattay and colleagues in the Journal of Immunology [1].GSE63432).

View Article: PubMed Central - PubMed

Affiliation: Division of Developmental Immunobiology, Tumor Immunology Program, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.

ABSTRACT
The establishment of central tolerance essentially depends on the promiscuous gene expression (pGE) of a plethora of tissue restricted antigens by the medullary thymic epithelial cells. The antigens are presented to developing thymocytes in the thymus to select for non-self reactive T-cell receptors in order to prevent autoimmune reactions in the periphery. However the molecular regulation of tissue-restricted antigen expression is still poorly understood. The only regulator known to play a role in the transcriptional regulation so far is the autoimmune regulator (AIRE). AIRE is thought to act in a multi-protein complex, promoting transcription, elongation and splicing of target genes. Yet the full composition of this Aire-associated multi-protein complex and its mode of action remain to be elucidated. Here we describe the experimental details and controls of the gene array analysis on the impact of the homeodomain-interacting protein kinase 2 (Hipk2) on promiscuous gene expression in medullary thymic epithelial cells based on the analysis of newly generated TEC-specific Hipk2 conditional knockout mice. The changes in gene expression are presumably mediated through a regulatory effect of Hipk2 on AIRE as published in the study by Rattay and colleagues in the Journal of Immunology [1]. The gene array data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE63432).

No MeSH data available.


Related in: MedlinePlus

Intensity controls comparing bead signals. (A) The signal intensity of the averaged housekeeping probes is shown in comparison to the signal intensity of all genes averaged. Shown is the mean with standard deviations, one of the two bead array chips is shown. (B) The signal intensity of the housekeeping gene probes is shown for each sample as mean values. (C) For each sample the signal intensity of all genes averaged is shown in comparison to the background signal levels. Shown are mean values.
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f0005: Intensity controls comparing bead signals. (A) The signal intensity of the averaged housekeeping probes is shown in comparison to the signal intensity of all genes averaged. Shown is the mean with standard deviations, one of the two bead array chips is shown. (B) The signal intensity of the housekeeping gene probes is shown for each sample as mean values. (C) For each sample the signal intensity of all genes averaged is shown in comparison to the background signal levels. Shown are mean values.

Mentions: Scanning of the microarray was done by using a Beadstation array scanner; settings were adjusted to a scaling factor of 1 and PMT settings at 430. The data extraction was done for all beads individually and outliers were removed when ≥ 2.5 MAD (median absolute deviation). All remaining data points were used for the calculation of the mean average signal for a given probe and the standard deviation for each probe was calculated. The gene expression intensity detected by the bead array was assessed for all samples (Fig. 1). The housekeeping signal intensity of all samples was above the averaged intensity of all genes within a sample. Further, the housekeeping and averaged all gene expression intensities were clearly separated from the background signal level.


Genome-wide gene expression profiling of homeodomain-interacting protein kinase 2 deficient medullary thymic epithelial cells.

Rattay K, Derbinski J, Hofmann TG, Kyewski B - Genom Data (2015)

Intensity controls comparing bead signals. (A) The signal intensity of the averaged housekeeping probes is shown in comparison to the signal intensity of all genes averaged. Shown is the mean with standard deviations, one of the two bead array chips is shown. (B) The signal intensity of the housekeeping gene probes is shown for each sample as mean values. (C) For each sample the signal intensity of all genes averaged is shown in comparison to the background signal levels. Shown are mean values.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664679&req=5

f0005: Intensity controls comparing bead signals. (A) The signal intensity of the averaged housekeeping probes is shown in comparison to the signal intensity of all genes averaged. Shown is the mean with standard deviations, one of the two bead array chips is shown. (B) The signal intensity of the housekeeping gene probes is shown for each sample as mean values. (C) For each sample the signal intensity of all genes averaged is shown in comparison to the background signal levels. Shown are mean values.
Mentions: Scanning of the microarray was done by using a Beadstation array scanner; settings were adjusted to a scaling factor of 1 and PMT settings at 430. The data extraction was done for all beads individually and outliers were removed when ≥ 2.5 MAD (median absolute deviation). All remaining data points were used for the calculation of the mean average signal for a given probe and the standard deviation for each probe was calculated. The gene expression intensity detected by the bead array was assessed for all samples (Fig. 1). The housekeeping signal intensity of all samples was above the averaged intensity of all genes within a sample. Further, the housekeeping and averaged all gene expression intensities were clearly separated from the background signal level.

Bottom Line: Yet the full composition of this Aire-associated multi-protein complex and its mode of action remain to be elucidated.The changes in gene expression are presumably mediated through a regulatory effect of Hipk2 on AIRE as published in the study by Rattay and colleagues in the Journal of Immunology [1].GSE63432).

View Article: PubMed Central - PubMed

Affiliation: Division of Developmental Immunobiology, Tumor Immunology Program, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.

ABSTRACT
The establishment of central tolerance essentially depends on the promiscuous gene expression (pGE) of a plethora of tissue restricted antigens by the medullary thymic epithelial cells. The antigens are presented to developing thymocytes in the thymus to select for non-self reactive T-cell receptors in order to prevent autoimmune reactions in the periphery. However the molecular regulation of tissue-restricted antigen expression is still poorly understood. The only regulator known to play a role in the transcriptional regulation so far is the autoimmune regulator (AIRE). AIRE is thought to act in a multi-protein complex, promoting transcription, elongation and splicing of target genes. Yet the full composition of this Aire-associated multi-protein complex and its mode of action remain to be elucidated. Here we describe the experimental details and controls of the gene array analysis on the impact of the homeodomain-interacting protein kinase 2 (Hipk2) on promiscuous gene expression in medullary thymic epithelial cells based on the analysis of newly generated TEC-specific Hipk2 conditional knockout mice. The changes in gene expression are presumably mediated through a regulatory effect of Hipk2 on AIRE as published in the study by Rattay and colleagues in the Journal of Immunology [1]. The gene array data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE63432).

No MeSH data available.


Related in: MedlinePlus