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Information


Unique identifier OMICS_18192
Name Oar
Alternative name Ovis aries reference
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Version 3.1
Maintained Yes

Maintainer


  • person_outline Emily Clark

Publication for Ovis aries reference

Oar citations

 (128)
library_books

Setup errors and effectiveness of Optical Laser 3D Surface imaging system (Sentinel) in postoperative radiotherapy of breast cancer

2018
Sci Rep
PMCID: 5940773
PMID: 29740104
DOI: 10.1038/s41598-018-25644-w

[…] marked by the surgery metal clips, postoperative serum swelling and surgical scars. The PTV-boost was defined as adding 7 mm margin to the CTV-boost and modified to be inside the PTV. Organ as risk (OAR) delineated were the lung, heart, and contralateral breast.Dose prescription was 57.5 Gy in 25 fractions for PTV-boost and 47.5 Gy in 25 fractions for PTV. The dosimetric objectives were to cover […]

library_books

Exploring the mechanisms of resistance to Teladorsagia circumcincta infection in sheep through transcriptome analysis of abomasal mucosa and abomasal lymph nodes

2018
PMCID: 5922024
PMID: 29703268
DOI: 10.1186/s13567-018-0534-x

[…] p with a depth of 30 million reads.The read quality of each sample was assessed using FastQC V_0.11.5 software []. The high quality read samples were later aligned against the ovine reference genome (Oar_v3.1) using the alignment software STAR_v2.5.2b []. We used the option –outSAMtype BAM Unsorted to obtain an unsorted bam file instead of the sam file obtained by default with the STAR software. T […]

library_books

Genome wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep

2018
Biosci Rep
PMCID: 5920141
PMID: 29439142
DOI: 10.1042/BSR20171350

[…] All downstream analyses were based on high-quality clean data. The transcriptome was assembled using Cufflinks (version 2.1.1) and Scripture based on reads mapped to the Ovis aries reference genome (Oar_v3.1). The assembled transcripts were annotated using the Cuffcompare program from the Cufflinks package. Unknown transcripts were used to screen for putative lncRNAs. Four computational approache […]

library_books

Cross species inference of long non coding RNAs greatly expands the ruminant transcriptome

2018
PMCID: 5926538
PMID: 29690875
DOI: 10.1186/s12711-018-0391-0

[…] sion atlas—of 54 mRNA-seq libraries—from 6-day old crossbred goats, which will be the subject of a dedicated analysis. For both species, each RNA-seq library was aligned against its reference genome (Oar v3.1 and ARS1, for sheep and goat, respectively) using HISAT2 [], with transcripts assembled using StringTie []. This pipeline produced a non-redundant set of de novo gene and transcript models, a […]

call_split

Genome Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds

2018
Front Genet
PMCID: 5902979
PMID: 29692799
DOI: 10.3389/fgene.2018.00118
call_split See protocol

[…] We annotated the genes associated with litter size in each breed using the O. aries assembly Oar_v.4.0. Further, we submitted the genes to the DAVID (database for annotation, visualization and integrated discovery) database for gene ontology (GO) enrichment and pathways analyses (,). The p-va […]

call_split

Genomic selection signatures in sheep from the Western Pyrenees

2018
PMCID: 5865298
PMID: 29566643
DOI: 10.1186/s12711-018-0378-x
call_split See protocol

[…] ng parameters: AVGQUAL:3 ILLUMINACLIP:TruSeq 3-PE-2.fa:2:30:10 MINLEN:31 LEADING:19 TRAILING:19 MINLEN:31. High-quality sequences were mapped against the domestic sheep reference assembly Ovis aries (OAR) v3.1 [] with Bowtie2 v2.2.3 [], using the –no-unal option. SAMtools v0.1.19 [] and Picard-tools v1.124 (http://broadinstitute.github.io/picard/) were used to convert between SAM and BAM formats ( […]

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Oar institution(s)
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, Scotland; Centre for Synthetic and Systems Biology, University of Edinburgh, Scotland
Oar funding source(s)
Supported by a Biotechnology and Biological Sciences Research Council (BBSRC) Grant BB/L001209/1 (‘Functional Annotation of the Sheep Genome’), the Institute Strategic Program Grants Farm Animal Genomics (BBS/E/D/20211550) and Transcriptomes, the Networks and Systems (BBS/E/D/20211552), a National Capability Grant (ARK-Genomics, BBS/E/D/20310000), the core grants from NERC (R8/H10/56), MRC (MR/K001744/1), the BBSRC (BB/J004243/1) and the Roslin Foundation.

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