Whole Exome Sequences from Iberian Roma samples
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ABSTRACT:
PROVIDER: EGAS00001004599 | EGA |
REPOSITORIES: EGA
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Project description:The Roma are the most numerous ethnic minority in Europe. The Iberian Roma arrived in the Iberian Peninsula five centuries ago and still today, they keep a strong group identity. Demographic and cultural reasons lie behind a high rate of Mendelian disease often related to founder variants. We have analysed exome data from 119 Iberian Roma individuals collected from 2018 to 2020. A database of variant frequency has been implemented (IRPVS) and made available online. We have analysed the carrier rate of founder private alleles as well as pathogenic variants present in the general population. Significant enrichment in structural variants involving gene clusters related to keratinization and epidermal growth suggest that evolutive mechanisms have developed towards climate and environmental adaptation. IRPVS can be accessed at http://irpvs.clinbioinfosspa.es/
| EGAS00001006758 | EGA
Project description:This study includes mitogenomes and whole nuclear genomes from prehistoric Iberian remains
| PRJEB29189 | ENA
Project description:The hypothalamus is implicated in controlling feeding and adiposity, besides many other physiological functions, and thus can be of great importance in explaining productive differences between lean and fatty pig breeds. The present study aimed to evaluate the hypothalamic transcriptome of pure Iberian (IBxIB) and Large White x Iberian crossbreds (IBxLW) at 60 days-old, produced in a single maternal environment. Results showed the implication of gender and genotype in the hypothalamic transcriptome, with 51 differentially expressed genes (DEGs) between genotypes and 10 DEGs between genders. Fourteen genotype by sex interactions were found, due to a higher genotype effect on transcriptome found in males. In fact, just 31 DEGs were identified when using only females but 158 using only males. A higher expression of genes related to mitochondrial activity in IBxIB male animals (ND3, ND4, ND5, UQCRC2 and ATP6) was found, which was related to a higher oxidative phosphorylation and greater reactive oxygen species and nitric oxide production. IBxLW male animals showed higher expression of SIRT3 regulator, also related to mitochondrial function. When females were analysed, no such differences were found, since only some differences in genes related to the tricitric acid cycle were observed. Thus, the results indicate a significant effect and interaction of the breed and the sex on the hypothalamic transcriptome at this early age.
2022-04-28 | GSE201408 | GEO
Project description:Growth is dependent on genotype and diet, even at early developmental stages. In this study, we investigated the effects of genotype, sex, and body weight on the fetal muscle transcriptome of purebred Iberian and crossbred Iberian x Large White pigs sharing the same uterine environment. RNA sequencing was performed on 16 purebred and crossbred fetuses with high body weight (340±14g and 415±14g, respectively) and 16 with low body weight (246±14g and 311±14g, respectively), on gestational day 77. Genotype had the greatest effect on gene expression, with 645 genes identified as differentially expressed (DE) between purebred and crossbred animals. Functional analysis showed differential regulation of pathways involved in energy and lipid metabolism, muscle development, and tissue disorders. In purebred animals, fetal body weight was associated with 35 DE genes involved in development, lipid metabolism and adipogenesis. In crossbred animals, fetal body weight was associated with 60 DE genes involved in muscle development, viability, and immunity. Interestingly, the results suggested an interaction genotype*weight for some DE genes. Fetal sex had only a modest effect on gene expression. This study allowed the identification of genes, metabolic pathways, biological functions and regulators related to fetal genotype, weight and sex, in animals sharing the same uterine environment. Our findings contribute to a better understanding of the molecular events that influence prenatal muscle development and highlight the complex interactions affecting transcriptional regulation during development.
2020-01-07 | GSE140460 | GEO
Project description:Characterising Mitochondrial Capture in an Iberian Shrew
| PRJEB57779 | ENA
Project description:The identification of genetic and epigenetic alterations from primary tumor cells has become a common method to identify genes critical to the development and progression of cancer. We provide a bioinformatic analysis of copy number variation and DNA methylation covering the genetic landscape of ovarian cancer tumor cells. We individually examined the copy number variation and DNA methylation for 44 primary ovarian cancer samples and 7 ovarian normal samples using our MOMA-ROMA technology and Affymetrix expression data as well as 379 tumor samples analyzed by The Cancer Genome Atlas. We have identified 346 genes with significant deletions or amplifications among the tumor samples. Utilizing associated gene expression data we predict 156 genes with significantly altered copy number and correlated changes in expression. We identify changes in DNA methylation and expression for all amplified and deleted genes. We predicted 615 potential oncogenes and tumor suppressors candidates by integrating these multiple genomic and epigenetic data types. This ROMA experiment was performed on Ovarian Tumor samples using the same platform as previously reported by Navin, N. et. al. Genome Res. 2010 Jan;20(1):68-80 (PMID: 19903760). Analysis of the array data was performed as previously reported in Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. (PMID: 18836286 ).
2011-10-17 | GSE28013 | GEO
Project description:We studied the influence of genetic type (pure Iberian pigs vs crossbred with Duroc) on l.dorsi transcriptome Background: The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in young animals of both genetic types, in order to identify genes, pathways and transcription factors responsible of their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DUxIB) were generated. Piglets (14 from each genetic type) were sacrificed at weaning (28 days) and longissimus dorsi muscle was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays. Results: Loin muscle composition showed significant differences between genetic types in intramuscular fat content (6% vs. 4.2% in IB and DUxIB animals, respectively, P=0.009) and in saturated and monounsaturated fatty acid contents (P=0.019 and P=0.044, respectively). Statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR<0.10), 102 upregulated in IB and 154 upregulated in DUxIB. The size of the effects ranged between 1.2x and 7.8x. Transcript differences were validated for a subset of DE genes by qPCR. Some candidate genes with known effects on muscle growth were found among the DE genes upregulated in DUxIB (IGF2, collagens, integrins). Genes related to lipid metabolism and proteolysis were found among the genes upregulated in IB (ME1, ELOVL6, caspases, catepsins, ubiquitination proteins). We observed alteration in biological functions related to extracellular matrix organization, cellular adhesion, muscle growth and lipid metabolism. Transcription factors (TF) potentially involved in the expression differences found were identified by calculating the regulatory impact factors (RIF). Sixteen TF were found, some of them with known relationship with muscle development (MSTN, SIX4), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these TF and DE genes show relevant differences between genetic types. Conclusion: The results contribute valuable information about molecular mechanisms determining the phenotypic differences of growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism. 28 male piglets were employed. 14 animals coming for pure Iberian parents and 14 coming from the crossing of Duroc boars with Iberian sows. Animals were sacrificed at 28 d of age. At the sacrifice, longissimus dorsi muscle tissue was sampled from each animal.
2014-06-11 | E-GEOD-53029 | biostudies-arrayexpress