Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Using RAD data to confirm parentage of polyploids in a reticulate complex of ferns

PROVIDER: PRJNA542715 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9050850.fastq.gz	Fastqsanger.gz
	SRR9050841.fastq.gz	Fastqsanger.gz
	SRR9050851.fastq.gz	Fastqsanger.gz
	SRR9050842.fastq.gz	Fastqsanger.gz
	SRR9050852.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 15

Similar Datasets

Project description:A 2b-RAD parentage analysis pipeline for complex and mixed DNA samples

| PRJNA754415 | ENA

Conservation and divergence of small RNA pathways in vascular plants revealed by small RNA analyses in lycophytes and ferns

Project description:Pathways underlying miRNA biogenesis, degradation, and activity were established early in land plant evolution, but the 24-nt siRNA pathway that guides DNA methylation was incomplete in early land plants, especially lycophytes. We show that the functional diversification of key gene families such as DICER-LIKE and ARGONAUTE (AGO) as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered an unexpected AGO family specific to lycophytes and ferns. Our phylogenetic analyses of miRNAs in lycophytes, bryophytes, ferns, and angiosperms refined the temporal origination of conserved miRNA families in land plants.

2017-07-20 | GSE98408 | GEO

Fern Database

Project description:Raw RNAseq data from ferns sampled in Singapore. Organ specific samples were selected for assembly via denovo assembly for comparative transcriptomics.

2024-03-01 | E-MTAB-13848 | biostudies-arrayexpress

Parentage Assignment in the Atlantic Salmon

Project description:RAD-seq data was used to generate SNP candidates for the development of a SNP parentage assignment panel.

| PRJEB17687 | ENA

RAD methods paper - Threespine Stickleback Lateral Plate Mapping

Project description:Restriction site Associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allow RAD tags to serve as genetic markers spread at a high-density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and utilizing an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second novel region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and non-model systems. Keywords: microarray genotyping

2007-01-24 | GSE5773 | GEO

Project description:Pteronia polyploids HybSeq

| PRJNA1071164 | ENA

Protein profiling of Chlamydia trachomatis growth forms

Project description:By comprehensive quantitative proteome analysis we characterize the three growth forms elementary body (EB), reticulate body (RB) and aberrant reticulate body (ARB) of Chlamydia trachomatis genital strain D/UW-3/CX

2017-01-04 | PXD003883 | Pride

Project description:ferns transcriptome

| PRJNA342359 | ENA

Project description:RAD-seq of Stewartia gemmata complex

| PRJNA1089257 | ENA

Simultaneous analysis of open chromatin, promoter interactions and gene expression in stimulated T cells implicates GWAS SNPs with causal genes

Project description:Genome-wide association studies have identified genetic variation contributing to complex disease risk but assigning causal genes and mechanisms has been more challenging, as disease-associated variants are often found in distal regulatory regions with cell-type specific behaviours. Here, the simultaneous correlation of ATAC-seq, Hi-C, Capture Hi-C and nuclear RNA-seq data, in the same stimulated T-cells over 24 hours, allowed the assignment of functional enhancers to genes. We show how small magnitude changes in DNA interaction and activity dynamics are correlated with much larger changes to dynamics in gene expression and that the strongest correlations are observed within 200 kb of promoters. Using rheumatoid arthritis as an exemplar T-cell mediated disease, we demonstrate interactions of expression quantitative trait locus SNPs with target genes and confirm assigned genes or show complex interactions for 20% of disease associated loci. Finally, we confirm one of the putative causal genes using CRISPR/Cas9.

2019-10-31 | GSE138767 | 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