Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nasonia vitripennis Genome Reference Panel 1.0

ABSTRACT: Collection of 34 inbred lines, derived from laboratory outbred Nasonia vitripennis HVRx population

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Nasonia Vitripennis

SUBMITTER: Wageningen University and Research, Laboraotry of Genetics

PROVIDER: PRJEB33514 | EVA | 2020-06-18

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	JGIL_10.filt.all.accessioned.vcf.gz	Vcf
	JGIL_10.filt.all.vcf.gz	Vcf
	JGIL_10.filt.all.vcf.gz.tbi	Vcf

Items per page:

1 - 3 of 3

Similar Datasets

Gene Expression Networks in the Drosophila Genetic Reference Panel

Project description:A major challenge of modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal phenotypes through networks of intermediate molecular phenotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences and mapped expression quantitative trait loci for annotated genes, novel transcribed regions (most of which are long noncoding RNAs), transposable elements and microbial species. We identified host variants affecting expression of transposable elements independent of copy number and microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination and are associated with transposable element expression. This study uncovers novel genetic features that regulate natural genetic variation of gene expression and generates testable hypotheses for future functional analyses.

2020-02-28 | GSE117850 | GEO

Liver gene expression in a panel of laboratory inbred mouse strains

Project description:This study aimed to perform gene expression quantitative trait locus mapping (eQTL) in the livers of a panel of 36 laboratory inbred strains. Mice were dosed with a saline solution by oral gavage and sacrificed at 24 hours. Livers were removed at sacrifice, RNA was extracted and gene expression was assayed using the Agilent G4121A array. Keywords: eQTL, mouse, liver

2009-02-28 | GSE14563 | GEO

RNA-Seq of mouse embryonic stem cells derived from genetically diverse inbred mouse strains

Project description:We measured genome-wide gene expression of embryonic stem cells derived from eight genetically diverse inbred mouse strains. We derived and cultured cells in LIF+2i media with feeders, and removed feeders prior to RNA collection. All lines were passage 6-8 when RNA was collected. We collected RNA from three biological replicate cell lines derived from each of the eight inbred mouse strains. For three strains (C57BL/6J, NOD, and PWD/PhJ), we obtained technical replicate RNA-Seq runs of each of the three biological replicate cell lines.

2020-08-13 | E-MTAB-7730 | biostudies-arrayexpress

Wing disc transcriptomic variation from 32 Drosophila genetic reference panel (DGRP) lines selected for a broad range of wing sizes

Project description:We performed RNA sequencing of wing discs at the wandering L3 larval stage from 32 inbred lines of Drosophila genetic reference panel (DGRP) that consists of 16 big and 16 small wing lines. We aimed to understand system-wide gene regulatory mechanisms that attain the observed natural variation in wing size including the sexual size dimorphism.

2019-02-18 | E-MTAB-7662 | biostudies-arrayexpress

Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics

Project description:Reference materials are vital to benchmarking the reproducibility of clinical tests and essential for monitoring laboratory performance for clinical proteomics. The reference material utilized for mass spectrometric analysis of the human proteome would ideally contain enough proteins to be suitably representative of the human proteome, as well as exhibit a stable protein composition in different batches of sample regeneration. Previously, The Clinical Proteomic Tumor Analysis Consortium (CPTAC) utilized a PDX-derived comparative reference (CompRef) materials for the longitudinal assessment of proteomic performance; however, inherent drawbacks of PDX-derived material, including extended time needed to grow tumors and high level of expertise needed, have resulted in efforts to identify a new source of CompRef material. In this study, we examined the utility of using a panel of seven cancer cell lines, NCI-7 Cell Line Panel, as a reference material for mass spectrometric analysis of human proteome. Our results showed that not only is the NCI-7 material suitable for benchmarking laboratory sample preparation methods, but also NCI-7 sample generation is highly reproducible at both the global and phosphoprotein levels. In addition, the predicted genomic and experimental coverage of the NCI-7 proteome suggests the NCI-7 material may also have applications as a universal standard proteomic reference. <ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/study-summary/S041">https://cptac-data-portal.georgetown.edu/study-summary/S041</a> on 12/08/21</li></ul>

2021-12-08 | MSV000088547 | MassIVE

Expression profiling of the Global Diversity Lines

Project description:The Global Diversity lines are a resource collection of 87 strains of Drosophila melanogaster (Grenier JK et al 2015. PMID 25673134). In this experiment, whole adult flies from the Global Diversity Lines (87 inbred lines derived from natural populations) were profiled using a spotted-oligo microarray to determine natural variation in gene expression patterns.

2016-03-17 | E-MTAB-4580 | biostudies-arrayexpress

Evaluation of NCI-7 Cell Line Panel

Project description:Reference materials are vital to benchmarking the reproducibility of clinical tests and essential for monitoring laboratory performance for clinical proteomics. The reference material utilized for mass spectrometric analysis of the human proteome would ideally contain enough proteins to be suitably representative of the human proteome, as well as exhibit a stable protein composition in different batches of sample regeneration. Previously, The Clinical Proteomic Tumor Analysis Consortium (CPTAC) utilized PDX-derived comparative reference (CompRef) materials for the longitudinal assessment of proteomic performance, however, inherent drawbacks of PDX-derived material has resulted in efforts to identify a new source of CompRef material. In this study, we examined the utility of using a panel of seven cancer cell lines, NCI-7 Cell Line Panel, as a reference material for mass spectrometric analysis of the human proteome. Our results showed that not only is the NCI-7 material suitable for benchmarking laboratory sample preparation methods, but NCI-7 sample generation is highly reproducible at both the global and phosphoprotein levels. In addition, the predicted genomic and experimental coverage of the NCI-7 proteome suggests the NCI-7 material may also have applications as a universal standard proteomic reference.

2018-05-14 | PXD008952 | Pride

Whole genome sequencing of experimental inbred chicken lines using pooled samples

Project description:Inbred chicken lines sequencing

| PRJEB51681 | ENA

129, AJ and Balb CGH against C57 reference on Agilent whole genome and custom mouse long oligonucleotide arrays

Project description:CGH comparing 3 inbred mouse strains to a C57BL/6 reference. The 3 inbred strains used have known trypanotolerance phenotypes, and these data were originally acquired as part of a study investigating the genetic mechanisms underlying trypanotolerance. These data have also been used in conjunction with the Perlegen 8 million SNP dataset to examine the effect of sequence mismatches on the log2 signal ratios acquired by these long oligonucleotide arrays. Keywords: comparative genomic hybridisation

2008-11-20 | GSE9669 | GEO

Distinct small RNA populations act antagonistically in formation of heterosis

Project description:This research reports the analysis of sRNAs in 14 and 7 inbred lines from a breeding population. We analyzed the contribution of sRNAs to the formation of heterosis via integrative association analysis with field data of 98 hybrids generated from the set of inbred lines. Our results indicate a contribution of sRNAs to heterosis. We were able to identify different sets of sRNAs associated with heterosis with distinct length and genome distribution patterns.

2016-10-24 | GSE51662 | 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