QqRhoAspi1
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB88609 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Analysis of genome-wide hydroxymethylation within infant placenta tissue collected at term. These samples have been collected from the Rhode Island Child Health Study (RICHS) cohort.
2021-01-04 | GSE144129 | GEO
Project description:Genome-wide profiling of placental DNA methylation in relation to neurobehavioral development. The Illumina 450k methylation array was used to profile 335 samples. These samples have been collected from the Rhode Island Child Health Study (RICHS).
2016-06-01 | GSE75248 | GEO
Project description:Genome-wide profiling of placental DNA methylation in relation to neurobehavioral development. The Illumina 450k methylation array was used to profile 335 samples. These samples have been collected from the Rhode Island Child Health Study (RICHS). Illumina analysis performed on 335 human placentas
2016-06-01 | E-GEOD-75248 | biostudies-arrayexpress
Project description:Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory regions. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as model animal for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosome regions that segregate for important agricultural and disease phenotypes. NimbleGen 385k whole genome tiling arrays were used to map CNVs in the chicken. This study has identified 96 CNVs in three lines of chickens (broiler, Leghorn and Rhode Island red). These CNVs encompass 16 Mb (1.3%) of the chicken genome. Twenty six CNVs were found in two or more animals. Smaller sized CNVs mostly affect none coding sequences while larger CNV regions involve genes, for example prolactin receptor, aldose reductase and zinc finger proteins, suggesting chicken CNVs potentially affect agricultural or disease related traits.
2010-06-11 | GSE19469 | GEO
Project description:Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform a genome-wide analysis of CNVs in the 12 diversified chicken genomes based on next-generation sequencing. We apply aCGH experiments to confirm our predicted CNVs. Results from aCGH agree well with our findings and the Pearson’s correlation values between the test and reference samples range from 0.644 to 0.722. The whole blood samples from Cornish, Rhode Island Red, and White Leghorn
2015-05-14 | E-GEOD-54118 | biostudies-arrayexpress
Project description:Airway epithelial cells from 3 different breeds of chicken infected with Newcastle Disease virus were sequenced and compared to cells from uninfected control birds. The 3 breeds were an indigenous breed, commercial Rhode Island Reds and a hybrid breed (Kenbro).
2015-01-19 | E-MTAB-3068 | biostudies-arrayexpress
Project description:Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory regions. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as model animal for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosome regions that segregate for important agricultural and disease phenotypes. NimbleGen 385k whole genome tiling arrays were used to map CNVs in the chicken. This study has identified 96 CNVs in three lines of chickens (broiler, Leghorn and Rhode Island red). These CNVs encompass 16 Mb (1.3%) of the chicken genome. Twenty six CNVs were found in two or more animals. Smaller sized CNVs mostly affect none coding sequences while larger CNV regions involve genes, for example prolactin receptor, aldose reductase and zinc finger proteins, suggesting chicken CNVs potentially affect agricultural or disease related traits. Blood DNA isolated from Cornish Rock, Leghorn and Rhode Island Red birds. Cy5 labeled DNA from a Cornish Rock male used as reference was mixed with Cy3 labeled DNA samples was then hybridized to the 385K chicken tiling array. Fluorescence intensity data were normalized with qspline algorithm and ratio data were analyzed with the circular binary segmentation algorithm from Olshen et al. Copy number variation calls were made if the averaged Log2 ratio of a segment was shifted by 0.3 from the baseline.
2010-06-11 | E-GEOD-19469 | biostudies-arrayexpress
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11830 | biostudies-arrayexpress