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Unknown,Transcriptomics,Genomics,Proteomics

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Somatic CNV profile of congenital ectopic thyroids

ABSTRACT: To assess whether specific genes have relevant somatic genetic or epigenetic alterations in ectopic tissue, we used a combined analysis of transcriptome (confirmed by qRT-PCR on 68 genes), methylome, structural genome variations (copy number variants, CNVs) and miRNA profile of ectopic compared with orthotopic thyroids. DNA form three ectopic thyroid compared with matched leucocytes.

ORGANISM(S): Homo sapiens

SUBMITTER: Johnny DeladoÃ«y

PROVIDER: E-GEOD-17463 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome, methylome and genomic variations analysis of ectopic thyroid glands.

Abu-Khudir Rasha R Paquette Jean J Lefort Anne A Libert Frederick F Chanoine Jean-Pierre JP Vassart Gilbert G Deladoëy Johnny J

PloS one 20101015 10

<h4>Background</h4>Congenital hypothyroidism from thyroid dysgenesis (CHTD) is predominantly a sporadic disease characterized by defects in the differentiation, migration or growth of thyroid tissue. Of these defects, incomplete migration resulting in ectopic thyroid tissue is the most common (up to 80%). Germinal mutations in the thyroid-related transcription factors NKX2.1, FOXE1, PAX-8, and NKX2.5 have been identified in only 3% of patients with sporadic CHTD. Moreover, a survey of monozygoti ...[more]

PMID: 20976176

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Methylome analysis of congenital ectopic thyroids

Project description:To assess whether specific genes have relevant somatic genetic or epigenetic alterations in ectopic tissue, we used a combined analysis of transcriptome (confirmed by qRT-PCR on 68 genes), methylome, structural genome variations (copy number variants, CNVs) and miRNA profile of ectopic compared with orthotopic thyroids. The MeDIP-chip was performed using pair of enriched methylated fraction (IP) and nomal fraction (IN) of genomic DNA from the three available cases and the three controls. The methylated fraction of genomic DNA was enriched using the methylated DNA immunoprecipitation (MeDIP) assay (Weber et al. Nat Genetics, 2005) and interrogated on human Promoter plus CpG Island Tiling Arrays with a ChIP design for CpG islands and promoter regions (n=28,226) from HG18 using 385,020 Probes selected from CGH probe bank with a median spacing of 101bp (Roche NimbleGen, Madison, WI).

2010-10-27 | E-GEOD-17581 | biostudies-arrayexpress

BCL6 ChIP on chip using a Nimblegen custom tiling array

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2010-06-10 | E-GEOD-7673 | biostudies-arrayexpress

Lamin b receptor regulates nuclear architecture and gene expression in olfactory neurons

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2012-08-30 | E-GEOD-38488 | biostudies-arrayexpress

Expression study of 'hemocyte minus vs hemocyte plus, and wounded vs unwounded hemocyte deficient' drosophila embryos

Project description:This SuperSeries is composed of the following subset Series: GSE10207: wounded versus nonwounded drosophila embryos GSE10208: hemocyte minus versus hemocyte plus drosophila embryos GSE10209: wounded vs unwounded hemocyte deficient embryos Keywords: SuperSeries Refer to individual Series

2010-05-22 | E-GEOD-10225 | biostudies-arrayexpress

wounded vs unwounded hemocyte deficient embryos

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2010-05-22 | E-GEOD-10209 | biostudies-arrayexpress

wounded versus nonwounded drosophila embryos

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hemocyte minus versus hemocyte plus drosophila embryos

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2010-05-22 | E-GEOD-10208 | biostudies-arrayexpress

Expression analysis of systemically infected Nicotiana benthamiana infected by South African cassava mosaic virus (SACMV)

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2013-01-17 | E-GEOD-43584 | biostudies-arrayexpress

Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium

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2015-12-31 | E-GEOD-47910 | biostudies-arrayexpress

Comparison of transcriptome between free-living and symbiotic cells of Frankia alni ACN14a

Project description:The actinobacteria Frankia alni is able to induce the formation of nodules on the root of a large spectrum of actinorhizal plants, where it converts dinitrogen to ammonia in exchange for plant photosynthates. In the present study, transcriptional analyses were performed on nitrogen-replete free-living cells and on Alnus glutinosa nodule bacteria, using whole genome microarrays. Distribution of nodule-induced genes on the genome was found to be mostly over regions with high synteny between three Frankia genomes, while nodule-repressed genes, which were mostly hypothetical and not conserved, were spread around the genome. Genes known to be related to symbiosis were highly induced: nif (nitrogenase), hup2 (hydrogenase uptake), suf (sulfur-iron cluster) and shc (hopanoids synthesis). The expression of genes involved in ammonium assimilation and transport was strongly modified suggesting that bacteria ammonium assimilation was limited. Genes involved in particular in transcriptional regulation, signalling processes, protein drug export, protein secretion, lipopolysaccharide and peptidoglycan biosynthesis that may play a role in symbiosis were also identified. We showed that this nodule transcriptome of Frankia was highly similar among phylogenetically distant plant families. To address gene expression changes of Frankia alni ACN in the symbiotic state, we compared transcript levels between young nodules formed on 4 species of trees (Alnus glutinosa, Alnus nepalensis, Myrica gale and Myrica rubra) and free-living cells grown in nitrogen-replete minimal medium. For A. glutinosa nodule and free-living cells, two sets of experiments (A and B) were performed in two different laboratories. Three biological replicates were preformed for each condition.

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