Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

N'Dama cattle Bionano Saphyr optical mapping

ABSTRACT: Project containing 2x N'Dama cattle (Bos taurus) 100X Bionano Saphyr optical mapping reads

PROVIDER: PRJEB47998 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Ndama_1_1628_RawMolecules.bnx.gz	Other
	ds677_NN031.bnx.gz	Other

Items per page:

1 - 2 of 2

Similar Datasets

N'Dama cattle (Bos taurus taurus) reference genome

Project description:Reference genome for the African N'Dama cattle (Bos taurus taurus) breed

| PRJEB41519 | ENA

Bos taurus strain:N'Dama

Project description:Bos taurus N'Dama breed genome sequencing

| PRJEA61193 | ENA

Optical mapping data for 16 cattle

Project description:Bionano optical mapping data for 16 cattle

| PRJEB52551 | ENA

Whole genome resequencing of three African N'Dama cattle (bos taurus)

Project description:Whole genome resequencing of three African N'Dama cattle (bos taurus) at 30X sequencing depth

| PRJEB39353 | ENA

Analysis of copy number variations among Chinese cattle breeds

Project description:Here we describe a genome-wide analysis of copy number variations (CNVs) in Chinese domestic cattle by using array comparative genomic hybridization (array CGH) and quantitative PCR (qPCR). We conducted array CGH analysis on 30 male cattle individuals, animals from consisting of 12 breeds of Bos taurus/Bos indicus, 1 Bos grunniens and and two ones of Bubalus bubalis breeds for with beef, and/or dairy or dual purpose. We identified over 470 candidate CNV regions (CNVRs) in Bos B. taurus/B. indicus; 118 candidate CNV regions (CNVRs) in B. grunniens, 139 CNVRs in B. bubalis. Furthermore, based on the Y haplotypes of B. taurus/ B. indicus, Wwe also identified 69, 337, and 251 candidate CNV regions (CNVRs) in the sub-groups of Y1, Y2 and Y3 haplotypes.

2014-12-30 | GSE47086 | GEO

Transcription profiling of horned and polled and scurs cattle

Project description:Transciprional profiling of horn forming region of Bos taurus comparing horned, polled and scurred cattle.

2010-05-01 | GSE21585 | GEO

Expression profiling of the host and the Ovine Herpesvirus 2 pathogen during malignant catarrhal fever of cattle

Project description:This SuperSeries is composed of the following subset Series: GSE13852: Expression profiling of Bos taurus lymph nodes upon infection with Ovine Herpesvirus 2 GSE13853: Expression profiling of Ovine Herpesvirus 2-infected lymph nodes from Bos taurus Refer to individual Series

2010-05-15 | E-GEOD-13854 | biostudies-arrayexpress

Population Structure, and Selection Signatures underlying High-Altitude Adaptation Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Cattle

Project description:Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp - 4,477,860 bp in size), covering ~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst=0.440) and STUB1 (Fst=0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst=0.222) and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.

2020-02-21 | GSE142218 | GEO