Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the assembly-versus-assembly method

ABSTRACT: 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.

ORGANISM(S): Sus scrofa

PROVIDER: GSE83910 | GEO | 2016/07/05

SECONDARY ACCESSION(S): PRJNA327417

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the assembly-versus-assembly method

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 piÃ©train 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

High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the whole-genome sequencing

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

High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the whole-genome sequencing

Project description:High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the whole-genome sequencing

| PRJNA508360 | ENA

Sus scrofa

Project description:High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the assembly-versus-assembly method

| PRJNA327417 | ENA

Genotyping of the PREDICT canola population by the Brassica 60K Illumina Infinium™ SNP genotyping array

Project description:477 spring-type Brassica napus (canola) lines from a hybrid breeding programme were genotyped using the Brassica Infinium™ 60k genotyping array.

2023-07-11 | E-MTAB-13142 | biostudies-arrayexpress

Refined Candidate Region for F4ab/ac Susceptibility situated proximal to MUC13 in Pigs

Project description:A GWAS study was then performed in 52 non-adhesive and 68 strong adhesive pigs for F4ab/ac ETEC originating from 5 Belgian farms. A new refined candidate region (chr13: 144,810,100-144,993,222) for F4ac ETEC susceptibility was identified with MUC13 adjacent to the distal part of the region. All pigs were phenotyped for the presence of the F4ab/ac receptor (F4ab/acR) using the in vitro villous adhesion assay with 4×108 F4ac E. coli (strain GIS26, serotype O149:K91, F4ac+) or F4ab E. coli (strain G7, serotype O8:K87, F4ab+) . A total of 120 F4ab/acR phenotyped pigs were genotyped using the Porcine SNP60 BeadChip (Illumina) containing 62,163 SNPs, according to the manufacturer’s protocol. The position of the SNPs was based on the current pig genome assembly (Sscrofa10.2).

2014-07-31 | E-GEOD-57981 | biostudies-arrayexpress

Project description:Identification of SNPs in alpacas using the Bovine HD Genotyping Beadchip

| PRJEB31129 | ENA

Multigene biomarkers of pyrethroid exposure: preliminary experiments: 60k microarrays

Project description:Multigene biomarkers of pyrethroid exposure: preliminary experiments: 60k microarrays

| PRJNA450651 | ENA

LIF-Dependent, Pluripotent Stem Cells Established from Inner Cell Mass of Porcine Embryos

Project description:The pig is important for agriculture and as an animal model in human and veterinary medicine, yet, despite over 20 years of effort, it has proved a difficult species from which to generate pluripotent stem cells analogous to those derived from mouse embryos. Here we report the production of LIF-dependent, so called naïve type, pluripotent stem cells from the inner cell mass of porcine blastocysts by up-regulating expression of KLF4 and POU5F1. These cells resemble mouse ES cells and are distinct from the FGF2-dependent, induced pluripotent cell type derived from porcine somatic cells. High throughput SNP chip genotyping was conducted on Illumina's Porcine SNP60 BeadChip (WG-410, a service provided by Geneseek, NE, http://www.neogen.com/GeneSeek/). The results exhibited that the two lines pluripotent stem cells from the inner cell mass of porcine blastocysts were porcine origin and genetically distinct.

2011-01-05 | GSE26436 | GEO

LIF-Dependent, Pluripotent Stem Cells Established from Inner Cell Mass of Porcine Embryos

2011-01-05 | E-GEOD-26436 | biostudies-arrayexpress