Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genotyping-by-sequencing of Douglas-fir (Pseudotsuga menziesii) provenances with ApeKI

ABSTRACT: Genotyping-by-sequencing of several coastal and interior Douglas-fir (Pseudotsuga menziesii) provenances with ApeKI as restriction enzyme

PROVIDER: PRJEB7733 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR674654_1.fastq.gz	Fastqsanger.gz
	ERR674654_2.fastq.gz	Fastqsanger.gz
	ERR674655_1.fastq.gz	Fastqsanger.gz
	ERR674655_2.fastq.gz	Fastqsanger.gz
	ERR674656_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 72

Similar Datasets

Transcriptome responses to natural environments in Pseudotsuga menziesii (Douglas-fir)

Project description:Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever-changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq). Using linear mixed models, we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80% of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction.

2016-09-20 | GSE73420 | GEO

Genotyping-by-sequencing of Douglas-fir (Pseudotsuga menziesii) provenances with ApeKI and HindIII

Project description:Genotyping-by-sequencing of several coastal and interior Douglas-fir (Pseudotsuga menziesii) provenances with ApeKI and HindIII as restriction enzymes

| PRJEB7737 | ENA

Transcriptome dynamics of the dormancy - growth transition in Douglas-fir needles

Project description:We report sequencing the transcriptome of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) during spring bud burst.

2013-06-05 | GSE44058 | GEO

Pseudotsuga menziesii var. glauca

Project description:Pseudotsuga menziesii var. glauca (interior douglas fir), vpPseMenz2

| PRJNA1131399 | ENA

Douglas-fir SeqCap-Exp

Project description:Sequence capturing experiment using five provenances of Douglas-fir (Pseudotsuga menziesii)

| PRJEB5165 | ENA

Pseudotsuga menziesii var. glauca

Project description:Pseudotsuga menziesii var. glauca (interior douglas fir) genomic and transcriptomic data

| PRJNA1131415 | ENA

Pseudotsuga menziesii var. glauca

Project description:Pseudotsuga menziesii var. glauca (interior douglas fir) genome assembly, vpPseMenz2, principal haplotype

| PRJNA1198709 | ENA

Pseudotsuga menziesii var. glauca

Project description:Pseudotsuga menziesii var. glauca (interior douglas fir) genome assembly, vpPseMenz2, alternate haplotype

| PRJNA1198710 | ENA

Pseudotsuga menziesii

Project description:Transcriptome responses to natural environments in Pseudotsuga menziesii (Douglas-fir)

| PRJNA296922 | ENA

Transcriptome dynamics of the dormancy - growth transition in Douglas-fir needles

Project description:We report sequencing the transcriptome of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) during spring bud burst. Samples from needle tissue of two half-sibs from two families each, nested within three seed sources, were sequenced (total of six families and 12 individuals). Samples were taken at seven time points with the failure of one library, resulting in 83 total sequenced samples. Three time points were used for transcriptome assembly and 4 time point were analyzed for differential expression across time and within seed sources.

2013-06-05 | E-GEOD-44058 | biostudies-arrayexpress

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