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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

Bead levels are compared between all samples. (A) Raw data bead levels of the arrays are shown. (B) Quantile normalized bead values of all samples are shown. Indicated are the quartiles (25–75%, lower boxes) and the maximum values (upper blue lines).
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f0010: Bead levels are compared between all samples. (A) Raw data bead levels of the arrays are shown. (B) Quantile normalized bead values of all samples are shown. Indicated are the quartiles (25–75%, lower boxes) and the maximum values (upper blue lines).

Mentions: The data were quantile normalized (Fig. 2) and differentially regulated genes were identified between HIPK2-deficient and control samples. The microarray analysis was performed in biological duplicates for mTEClow and mTEChigh fractions on the Hipk2ko and control background. Genes with a fold change of ≥ 2 or ≤ 0.5 and with a p-value ≤ 0.0005 were considered to be differentially expressed. Statistical T-test calculation was performed in R, Benjamini-Hochberg correction is applied over all p-values of the differential expression analysis. The microarray data were deposited in GEO under accession number GSE63432.


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)

Bead levels are compared between all samples. (A) Raw data bead levels of the arrays are shown. (B) Quantile normalized bead values of all samples are shown. Indicated are the quartiles (25–75%, lower boxes) and the maximum values (upper blue lines).
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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

f0010: Bead levels are compared between all samples. (A) Raw data bead levels of the arrays are shown. (B) Quantile normalized bead values of all samples are shown. Indicated are the quartiles (25–75%, lower boxes) and the maximum values (upper blue lines).
Mentions: The data were quantile normalized (Fig. 2) and differentially regulated genes were identified between HIPK2-deficient and control samples. The microarray analysis was performed in biological duplicates for mTEClow and mTEChigh fractions on the Hipk2ko and control background. Genes with a fold change of ≥ 2 or ≤ 0.5 and with a p-value ≤ 0.0005 were considered to be differentially expressed. Statistical T-test calculation was performed in R, Benjamini-Hochberg correction is applied over all p-values of the differential expression analysis. The microarray data were deposited in GEO under accession number GSE63432.

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