Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fine mapping of a QTL for number of teats

ABSTRACT: SNP detection in a QTL region for number of teats

INSTRUMENT(S): -

ORGANISM(S): Sus Scrofa

SUBMITTER: Norsvin

PROVIDER: PRJEB27233 | EVA | 2018-06-11

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	out_teats_d_filtered1.eva1.1.accessioned.reaccession.vcf.gz	Vcf
	out_teats_d_filtered1.eva1.1.accessioned.vcf.gz	Vcf
	out_teats_d_filtered1.eva1.1.vcf.gz	Vcf
	out_teats_d_filtered1.eva1.1.vcf.gz.tbi	Vcf
	out_teats_l_filtered1.eva1.1.accessioned.reaccession.vcf.gz	Vcf

Items per page:

1 - 5 of 8

Similar Datasets

Identification of candidate genes involved in salt stress response at germination and seedling stages by QTL mapping in upland cotton

Project description:Salinity is a major abiotic stress at critical stages of seed germination and seedling establishment. Germination rate (GR) and field emergence rate (FER) are the key traits that determine the basic number of plants stand under field conditions. To explore molecular mechanisms in upland cotton under salt stress, a population of 177 recombinant inbred lines (RILs) and their parents were evaluated for seed germination traits (GP, germination potential; GR; FW, fresh weight; DW, dry weight; GL, germinal length) and seedling traits (FER; SH, seedling height; NL, Number of main stem leaves) in 2016-2018. Based on the linkage map contained 2,859 single nucleotide polymorphism (SNP) and simple sequence repeats (SSR) markers, traits under salt stress (E1) and normal condition, (E2) and the converted relative index (R-value) of three years’ trials were used to map quantitative trait loci (QTL). A total of three QTL and two clusters were detected as salt-tolerant QTL. Three QTL (qGR-Chr4-3, qFER-Chr12-3, qFER-Chr15-1) were detected under salt stress and R-value, which explained phenotypic variance of 9.62%-13.67%, and 4.2%-4.72%, 4.75%-8.96%, respectively. Two clusters (Loci-Chr4-2 and Loci-Chr5-4) harboring the QTL for four germination traits (GR, FER, GL, NL) and six seedling traits (GR, FER, DW, FW, SH, NL) were detected related under salt stress. A total of 691 genes were found in the candidate QTL or clusters. Among them, four genes (Gh_A04G1106, Gh_A05G3246, Gh_A05G3177, Gh_A05G3266) showed expression changes between sensitive and tolerant lines under salt stress, and were assigned as candidate genes in response to salt stress. The consistent salt-tolerance QTL identified in both germination and seedling stages will facilitate new information for cotton breeding.

2022-06-23 | GSE186533 | GEO

Ultra-high-density QTL markers mapping for seedling photomorphogenesis mediating Arabidopsis establishment in southern Patagonia

Project description:The intent of the experiment was to construct molecular SNP-binning markers of a Col-0 x Pat RIL population, for sensitive QTL mapping. We performed Illumina low-coverage DNA sequencing of plant tissues.

2021-07-21 | E-MTAB-10387 | biostudies-arrayexpress

Functional dissection of QTL-region affecting fat-deposition

Project description:Functional dissection of QTL-region affecting fat-deposition

2018-10-15 | E-MTAB-1434 | biostudies-arrayexpress

High-resolution mapping of copy-number alterations with massively parallel sequencing

Project description:In order to benchmark the reproducibility of Affymetrix Genome-Wide Human SNP Array 6.0 for detecting copy-number alterations, we performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numbers at each SNP probeset by a custom copy-number pipeline (PMID: 18772890). For each cell line, copy number data from replicate arrays are supplied in the accompanying matrix files. For each SNP probeset, we calculated the median copy number across replicate arrays. We compared the copy-number alterations detected by Circular Binary Segmentation segmentation of these arrays with statistical analyses of short sequence reads obtained from the Illumina/Solexa 1G GenomeAnalyzer. Shotgun sequencing results can be found in the NCBI Short Read Archive, accession number SRP000246 Keywords: disease state analysis

2008-11-14 | GSE13372 | GEO

Expression QTL mapping of Toxoplasma gondii genes

Project description:This SuperSeries is composed of the following subset Series: GSE11437: Expression QTL mapping of Toxoplasma gondii genes, Bradyzoite array GSE11514: Expression QTL mapping of Toxoplasma gondii genes, Tachyzoite array Keywords: SuperSeries Refer to individual Series

2008-05-22 | E-GEOD-11515 | biostudies-arrayexpress

Expression QTL mapping of chicken femoral bone

Project description:Expression quantitative trait locus (QTL) mapping of 127 adult femoral bone samples from a Red Junglefowl x White Leghorn advanced intercross line. Bone trait QTL have been mapped in the same cross, allowing a genetical genomics approach to quantitative trait gene identification

2015-10-31 | E-MTAB-3141 | biostudies-arrayexpress

Copy number variation analysis of a fetus with Silver-Russell syndrome in China

Project description:The Affymetrix CytoScan 750K Array chip contains 200000 SNP markers and 550000 CNV markers, distributed across the entire human genome at an average density of approximately 1 marker/4kb (not covering all loci of the entire chromosome genome). It is used to detect clinically significant chromosomal microdeletions/microduplications, chromosomal subtelomer deletion syndrome, and other abnormal chromosomal copy number variations (CNVs) as well as loss of heterozygosity (LOH). In a case study of Zhangzhou Municipal Hospital of Fujian Province, copy number variation detection was performed on a fetus with Silver-Russell syndrome using CytoScan 750K Array chip, and variations in the corresponding region were identified.

2024-12-11 | GSE283758 | GEO

Expression QTL mapping of chicken hypothalamus

Project description:Gene expression QTL mapping of 129 individual hypothalamus samples from a Red Junglefowl by White Leghorn advanced intercross

2015-11-29 | E-MTAB-3154 | biostudies-arrayexpress

Detection of de novo and homozygous copy number variants in 99 autism simplex trios

Project description:Comparison of whole genome exome array CGH to a commercial SNP array for detection of de novo and homozygous copy number variants in 99 autism simplex trios. Will update once manuscript is prepared.

2011-04-30 | GSE23765 | GEO

Fine-scale mapping of copy-number alterations with massively parallel sequencing

Project description:In order to benchmark the reproducibility of Affymetrix 238K Sty arrays for detecting copy-number alterations. We performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numbers at each SNP probeset by array pre-processing with the GISTIC algorithm (PMID: 18077431). For each SNP probeset, we calculated the median copy number across replicate arrays. The median copy number profile for each tumor cell line was segmented with the GLAD algorithm (PMID: 15381628) to partition the genome into regions of constant copy number. We compared the copy-number alterations detected by GLAD segmentation of these arrays with statistical analyses of short sequence reads obtained from the Illumina/Solexa 1G GenomeAnalyzer. Shotgun sequencing results can be found in the NCBI Short Read Archive, accession number SRP000246. Keywords: disease state analysis

2008-11-14 | GSE12019 | 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