Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

53 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Aristaeus chip 1.0: an in situ synthesized oligonucleotide microarray for Ovis aries

ABSTRACT: Here we present a high-density in situ synthesized microarray for Ovis aries, named Aristaeus, designed by means of a pipeline of software instruments that, starting from non-annotated redundant EST sequences, selects oligonucleotides suitable for in situ generation on chip. The chip was tested by comparing the gene expression profiles of two sheep breeds with different phenotype, Sarda and Gentile di Puglia. We carried out microarray experiments on liver and udder tissues from lactating individuals and identified a relevant number of differentially expressed genes, all involved in metabolism pathways. The results are consistent with literature knowledge, while selected differential gene expressions have been confirmed by quantitative real-time polymerase chain reaction analyses. Tissue samples of liver were collected from 4 lactating individuals of two sheep (Ovis aries) breeds, Gentile di Puglia and Sarda. Biopsies of liver tissue were taken at second lactation stage (first record, stage 01: 6 days after lambing; second record, stage 02: 44 days after lambing) in both breeds. Tissues from liver were immersed in RNAlater (Sigma) immediately after biopsy and stored at -20°C. Samples were pooled by breed and then reverse labeled (cy5 and cy3), resulting in four raw data sets.

ORGANISM(S): Ovis aries

SUBMITTER: Alessio Valentini

PROVIDER: E-GEOD-31044 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A Tool for Sheep Product Quality: Custom Microarray from Public Databases

Project description:Milk and dairy products are an essential food and an economic resource in many countries. Milk component synthesis and secretion by the mammary gland involve expression of a large number of genes whose nutritional regulation remains poorly defined. We aim at understanding the genomic influence on milk quality and synthesis by comparing two sheep breeds, with different milking attitude, Sarda and Gentile di Puglia, using sheep-specific microarray technology. From sheep ESTs deposited at NCBI, we generated the first annotated microarray developed for sheep with a covering of most of the genome. Whole tissue samples of mammary gland were collected from 4 lactating individuals of two sheep (Ovis aries) breeds, Gentile di Puglia and Sarda. Biopsies of lactating mammary tissue were taken at two lactation stages (first record, stage 01: 6 days after lambing; second record, stage 02: 44 days after lambing) in both breeds. Tissues from mammary gland were immersed in RNAlater (Sigma) immediately after biopsy and stored at -20Â°C.

2010-05-19 | E-GEOD-18619 | biostudies-arrayexpress

Aristaeus chip 1.0: an in situ synthesized oligonucleotide microarray for Ovis aries

Project description:Here we present a high-density in situ synthesized microarray for Ovis aries, named Aristaeus, designed by means of a pipeline of software instruments that, starting from non-annotated redundant EST sequences, selects oligonucleotides suitable for in situ generation on chip. The chip was tested by comparing the gene expression profiles of two sheep breeds with different phenotype, Sarda and Gentile di Puglia. We carried out microarray experiments on liver and udder tissues from lactating individuals and identified a relevant number of differentially expressed genes, all involved in metabolism pathways. The results are consistent with literature knowledge, while selected differential gene expressions have been confirmed by quantitative real-time polymerase chain reaction analyses.

2013-02-05 | GSE31044 | GEO

Analysis of copy number variations by SNP50 BeadChip array in Chinese sheep

Project description:The sheep (Ovis aries) plays a major socio-economic role in the world. Copy number variations (CNVs) are increasingly recognized as a key and potent source of genetic variation and phenotypic diversity, but little is known about the extent to which CNVs contribute to genetic variation in Chinese sheep breeds. Analyses of CNVs in the genomes of eight sheep breeds were performed using the sheep SNP50 BeadChip genotyping array. A total of 111 CNV regions (CNVRs) were obtained from 160 Chinese sheep breeds. These CNVRs covered 13.75 Mb of the sheep genome sequence. A total of 22 Go terms and 17 candidate genes were obtained from the functional analysis. Ten CNVRs were selected for validation, of which 7 CNVRs were further experimentally confirmed by quantitative PCR. Four candidate genes were selected to confirm the results of the functional analysis. These results provide a resource for furthering understanding of ruminant biology, and for further improving the genetic quality of sheep breeds.

2017-10-01 | GSE71584 | GEO

Project description:Ovis aries(Hu sheep) liver transcriptome

| PRJNA822707 | ENA

Sheep milk transcriptome

Project description:This study presents a dynamic characterization of the sheep milk transcriptome aiming at achieving a better understanding of the sheep lactating mammary gland. Transcriptome sequencing (RNA-seq) was performed on total RNA extracted from milk somatic cells from ewes on days 10, 50, 120 and 150 after lambing. The experiment was performed in Spanish Churra and Assaf breeds, which differ in their milk production traits. Nearly 67% of the annotated genes in the reference genome (Oar_v3.1) were expressed in ovine milk somatic cells. For the two breeds and across the four lactation stages studied, the most highly expressed genes encoded caseins and whey proteins. We detected differentially expressed genes (DEGs) across lactation points, with the largest differences being found, between day 10 and day 150. Upregulated GO terms at late lactation stages were linked mainly to developmental processes linked to extracellular matrix remodeling. A total of 256 annotated DEGs were detected in the Assaf and Churra comparison. Some genes selectively upregulated in the Churra breed grouped under the endopeptidase and channel activity GO terms. These genes could be related to the higher cheese yield of this breed. Overall, this study provides the first integrated overview on sheep milk gene expression.

2016-06-07 | GSE74825 | GEO

Characterization of Sheep Milk Extracellular Vesicle-miRNA by Sequencing and Comparison with Cow milk

Project description:Milk can mediate maternal-neonatal signal transmission by the bioactive component-extracellular vesicles (EVs), which select specific types of miRNA to encapsulate. The miRNA profiling of sheep milk EVs was characterized by sequencing and compared with that of cow milk. Sheep milk EVs contained various small RNAs, including tRNA, Cis-regulatory element, rRNA, snRNA, other Rfam RNA, and miRNA, which held about 36% of all the small RNAs. Totally 84 types of miRNAs were annotated with Ovis aries by miRBase (version 22.0) in sheep milk EVs, with 75 shared types of miRNAs in all samples. Fourteen sheep milk EV-miRNAs in the top 20, occupying 98% of the total expression, were immune-related.

2020-01-17 | GSE143779 | GEO

Ovis aries breed:sheep

Project description:ovis aries csn3 exon 4 sequencing in senegalese sheep breeds

| PRJNA885040 | ENA

Ovis aries

Project description:Whole Genome Resequencing data of Portuguese sheep breeds (Ovis aries)

| PRJNA764662 | ENA

Identification and characterization of microRNAs in the intestinal tissues of sheep (Ovis aries)

Project description:Here, we analyzed and identified the miRNA expression profile of three different intestinal tissues (i.e., duodenum, cecum, and colon) of sheep (Ovis aries) using high-throughput sequencing and bioinformatic methods. In total, 128 known miRNAs were identified, 526 novel miRNAs were predicted, and 202 differentially expressed miRNAs were found between the different tissues. Additionally, 4,422 candidate target genes were predicted, and 185 non-redundant GO annotation terms were identified using enrichment analysis. A total of 529 target genes were found to participate in 37 KEGG biological pathways, and 270 of these genes were significantly enriched in the metabolism category.

2018-03-07 | GSE100649 | GEO

Transcriptional analysis of adipose tissue during post-natal development reveals depot-specific responsiveness to maternal dietary supplementation

Project description:In this study we use ovis aries as a comparative model The objective of the study was to compared changes in genetic interactions in five adipose tissue deposits during early development.

2018-06-15 | GSE115799 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data