Ontology highlight
ABSTRACT:
PROVIDER: PRJNA858995 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Porcine 60K BeadChip genotyping arrays (Illumina) are increasingly being applied in pig genomics to validate SNPs identified by re-sequencing or assembly-versus-assembly method. Here we report that more than 98% SNPs identified from the porcine 60K BeadChip genotyping array (Illumina) were consistent with the SNPs identified from the assembly-based method. This result demonstrates that whole-genome de novo assembly is a reliable approach to deriving accurate maps of SNPs. To compare SNPs identified by genotyping arrays and de novo assembly method, we genotyped 10 pig breeds by porcine 60K BeadChip genotyping array (Illumina), including 1 berkshire pig, 1 hampshire pig, 1 landrace pig, 1 large white pig,1 piétrain pig, 1 bamei pig,1 jinhua pig, 1 meishan pig, 1 rongchang pig and 1 Tibetan wild boar.
2016-07-05 | E-GEOD-83910 | biostudies-arrayexpress
Project description:Ossabaw Pig genome project
| PRJNA845129 | ENA
Project description:A CNV map in pigs could facilitate the identification of chromosomal regions that segregate for important economic and disease phenotypes. The goal of this study was to identify CNV regions (CNVRs) in pigs based on a custom array comparative genome hybridization (aCGH). We carried out a custom-made array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the pig genome analysing animals of diverse pig breeds (White Duroc, Yangxin, Erhualian, Tongcheng, Large White, Pietrain, Landrace and Chinese new pig line DIV ) using a tiling oligonucleotide array with ~720,000 probes designed on the pig genome (Sus scrofa genome version 9.0).
2013-08-09 | GSE41488 | GEO
Project description:The wide application of pig disease model has caused a surge of interest in the study of derivation of pig induced pluripotent cells (iPSCs). Here we performed genome-wide analysis of gene expression profiling by RNA-seq and small RNA-seq and DNA methylation profile by MeDIP-seq in pig iPSCs through comparison with somatic cells. We identified mRNA and microRNA transcripts that were specifically expressed in pig iPSCs. We then pursued comprehensive bioinformatics analyses, including functional annotation of the generated data within the context of biological pathways, to uncover novel biological functions associated with maintenance of pluripotency in pig. This result supports that pig iPS have transcript profiles linked to ribosome, chromatin remodeling, and genes involved in cell cycle that may be critical to maintain their pluripotency, plasticity, and stem cell function. Our analysis demonstrates the key role of RNA splicing in regulating the pluripotency phenotype of pig cells. Specifically, the data indicate distinctive expression patterns for SALL4 spliced variants in different pig cell types and highlight the necessity of defining the type of SALL4 when addressing the expression of this gene in pig cells. MeDIP-seq data revealed that the distribution patterns of methylation signals in pig iPS and somatic cells along the genome. We identify 25 novel porcine miRNA, including pluripotency-related miR-302/367cluster up-regulated in pig iPSCs. At last, we profile the dynamic gene expression signature of pluripotent genes in the preimplantation development embryo of pig. The resulting comprehensive data allowed us to compare various different subsets of pig pluripotent cell. This information provided by our analysis will ultimately advance the efforts at generating stable naive pluripotency in pig cells.
2016-01-07 | E-MTAB-2643 | biostudies-arrayexpress
Project description:Crossbreeding has been an effective method to improve crossbred performance in pig industry. To have a global view of a classic three-way crossbreeding system of Duroc x (Landrace x Yorkshire) (DLY), we identified SNPs for each pig breed and crossbred individual originated from a DLY pig family to estimate the influence of purebreds on crossbred offspring using whole-genome sequencing. To confirm the accuracy of the SNPs identified by whole-genome sequencing, therefore, we performed the porcine 60K BeadChip genotyping array (Illumina) for each sequenced pig individual.
2018-12-05 | GSE123327 | GEO
Project description:In mammals, ovarian folliculogenesis leading to the ovulation of completely mature oocytes is a long and complex process that is regulated at different levels. The mechanisms that underlie the selection of one or several dominant follicles as well as the regulation of the number of ovulating follicles are largely unknown. In this project, we proposed to study the genetic determinism that underlies the difference of ovulation rate between species (cattle and pigs). Towards this purpose, we made a comparative transcriptomics study on granulosa cells. Pig and cattle comparison was achieved by a transcriptome analysis with a 9K nylon pig microarray (GPL3729) on granulosa cells from either small healthy antral follicles (SHF) or large healthy antral follicles (LHF). The images were quantified using AGscan software and the data were managed with BASE software. Statistical analysis was performed using R software. Transcriptomic analysis on pig and cattle evidenced 252 differentially expressed genes (FDR5%) between the two follicle classes and/or the two species. This research project which implicated three laboratories from INRA: « Laboratoire de Génétique Cellulaire » (UMR444-LGC) , « Station d’Amélioration Génétique des Animaux » (UR 631-SAGA) and « Physiologie des Comportements et de la reproduction » (UMR 85-PRC) benefited from both European funding through SABRE project and French ANR funding through GenOvul project. Keywords: transcriptome analysis, pig, cattle, ovary, folliculogenesis, gene expression, cDNA microarray
2012-12-31 | GSE23335 | GEO