Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1142724 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We carried out a cross species cattle-sheep array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the sheep genome analysing animals of Italian dairy breeds (Sarda, Bagnolese, Laticauda, Massese and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs) covering about 10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and median equal to 77.6 kb and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in the cattle and goat genomes indicated that overlaps between sheep and goat and sheep and cattle CNVRs are highly significant (P<0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs.
2010-11-16 | GSE25122 | GEO
Project description:We carried out a cross species cattle-sheep array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the sheep genome analysing animals of Italian dairy breeds (Sarda, Bagnolese, Laticauda, Massese and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs) covering about 10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and median equal to 77.6 kb and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in the cattle and goat genomes indicated that overlaps between sheep and goat and sheep and cattle CNVRs are highly significant (P<0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs. In this study we made use of the high conservation and homology between the cattle and sheep genomes determined by their phylogenetic closeness to identify CNVs in sheep applying the same approach we carried out to identify CNVs in the goat genome. We used a custom tiling array including ~385,000 oligonucleotide probes designed on the Btau_4.0 version of the Bos taurus genome assembly and analysed genomic DNA samples of 11 sheep belonging to 6 different Italian dairy sheep breeds (2 Sarda, 2 Bagnolese, 2 Comisana, 2 Massese, 2 Laticauda and 1 Valle del Belice) compared to the reference DNA of another Sarda sheep.
2010-11-16 | E-GEOD-25122 | biostudies-arrayexpress
Project description:Artificial insemination in small ruminants is most commonly performed using fresh semen due to the low fertility rates typically achieved with frozen spermatozoa. Usually, when developing and applying assisted reproductive technologies, sheep and goats are often lumped together as one specie. In order to optimize sperm cryopreservation protocols in sheep and goat, differences in sperm proteomics between ram and buck are necessary to detect, which may contribute to differences in sperm function and fertility.
2020-05-26 | PXD014095 | Pride
Project description:In the present study, the whole cell protein extracts of B. abortus and B. melitensis were separated using SDS-PAGE and western blotting was carried out with the antiserum from naturally infected host animals (cow, buffalo, goat and sheep). The proteins bands that matched with western blot signals were excised, trypsin digested and subjected to MALDI identification.
2014-12-01 | PXD001270 | Pride
Project description:Background The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi, Girgentana, and Murciano-Granadina) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. Results We identified a total of 161 CNVs (an average of 17.9 CNVs per goat), with the largest number in the Saanen breed and the lowest in the Camosciata delle Alpi goat. By aggregating overlapping CNVs identified in different animals we determined CNV regions (CNVRs): on the whole, we identified 127 CNVRs covering about 11.47 Mb of the virtual goat genome referred to the bovine genome (0.435% of the latter genome). These 127 CNVRs included 86 loss and 41 gain and ranged from about 24 kb to about 1.07 Mb with a mean and median equal to 90,292 bp and 49,530 bp, respectively. To evaluate whether the identified goat CNVRs overlap with those reported in the cattle genome, we compared our results with those obtained in four independent cattle experiments. Overlapping between goat and cattle CNVRs was highly significant (P<0.0001) suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Genes with environmental functions were over-represented in goat CNVRs as reported in other mammals. Conclusions We describe a first map of goat CNVRs. This provides information on a comparative basis with the cattle genome by identifying putative recurrent interspecies CNVs between these two ruminant species. Several goat CNVs affect genes with important biological functions. Further studies are needed to evaluate the functional relevance of these CNVs and their effects on behavior, production, and disease resistance traits in goats.
2010-11-09 | GSE24436 | GEO
Project description:A comparative genomic approach was used to identify large sequence polymorphisms among Mycobacterium avium isolates obtained from a variety of host species. DNA microarrays were used as a platform for comparing mycobacteria field isolates with the sequenced bovine isolate Mycobacterium avium subsp. paratuberculosis (Map) K10. ORFs were classified as present or divergent based on the relative fluorescent intensities of the experimental samples compared to Map K10 DNA. Map isolates cultured from cattle, bison, sheep, goat, avian, and human sources were hybridized to the Map microarray. Three large deletions were observed in the genomes of four Map isolates obtained from sheep and four clusters of ORFs homologous to sequences in the Mycobacterium avium subsp. avium (Maa) 104 genome were identified as being present in these isolates. One of these clusters encodes glycopeptidolipid biosynthesis enzymes. One of the Map sheep isolates had a genome profile similar to a group of Mycobacterium avium subsp. silvaticum (Mas) isolates which included four independent laboratory stocks of the organism traditionally identified as Maa strain 18. Genome diversity in Map appears to be mostly restricted to large sequence polymorphisms that are often associated with mobile genetic elements. Keywords: Comparative genomic hybridization
2007-04-27 | GSE7622 | GEO
Project description:We performed mRNA-seq on 27 samples from the three tissues (heart, liver and kidney) across three species (cattle, sheep, goat)
2017-09-06 | GSE77020 | GEO
Project description:Whole genome sequencing of polycerate sheep and goat
| PRJEB39341 | ENA
Project description:The study confirmed a batch of goat skin and hair follicles miRNA, by high-throughput sequencing methods.316 sequences miRNAs were obtained by the means of analysis and we confirmed the authenticity of 68 known miRNAs and discovered 248 novel miRNAs, as well as 22 miRNAs that haven’t been reported before. Through the miRNAs family analysis, we found the co-expressed miRNAs in goat and sheep located in the same region of chromosome, which may play an essential role in skin and follicle development. In addition, the prediction of novel target miRNAs followed by the analysis of target gene pathways indicated that MAPK pathway may have an important effect to the fast growth of skin follicle cell.
2012-02-25 | GSE36052 | GEO
Project description:We have used RNA-Seq to examine expression profiles of different subsets of PBMCs-CD4+, CD8+, CD14+, CD21+, CD335+ from Goat and Sheep under sungri/96 PPRV vaccination.
2021-02-19 | GSE155504 | GEO