Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: WGBS of maize inbreds

PROVIDER: PRJNA400328 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5980380.fastq.gz	Fastqsanger.gz
	SRR5980380_1.fastq.gz	Fastqsanger.gz
	SRR5980380_2.fastq.gz	Fastqsanger.gz
	SRR6201710_1.fastq.gz	Fastqsanger.gz
	SRR6201710_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 27

Similar Datasets

Gene expression variation among eight maize inbreds

Project description:Expression profiling analyses for eight maize inbreds reveals extensive transcriptional variation. Many genes exhibit presence-absence variation among the inbred lines. Keywords: Genotype comparison series

2008-01-26 | GSE10237 | GEO

Gene expression variation among eight maize inbreds - 70mer oligo array

Project description:Expression profiling analyses for eight maize inbreds reveals extensive transcriptional variation. This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10237). Keywords: Genotype comparison series

2008-02-22 | GSE10543 | GEO

The clock-mediated transcriptional regulatory networks contribute to biomass heterosis in maize

Project description:we determine genome-wide binding profiles of a maize CCA1 homolog, ZmCCA1b, in maize inbreds and F1 hybrids at different times of the day. ZmCCA1b is characterized as a central clock regulator gene with evolutionarily conserved molecular and circadian functions and nonadditively expressed in F1 hybrid seedlings. ZmCCA1b binds to over 4,300 target genes in the maize genomes, of which annotation confirms energy metabolic pathways as the main output. We report that an altered temporal binding activity of ZmCCA1b in the hybrid seedlings, which increases expression of carbon fixation genes, increases carbon fixation rates and biomass, demonstrating a novel example of how circadian-regulatory networks directly contribute to growth vigor in maize hybrids. These results collectively offer new insights into clock-mediated regulation of growth vigor in hybrid plants and crops. Profiling genome-wide binding events of ZmCCA1b in the maize inbreds and F1 hybrids at ZT3, ZT9 and ZT15 using chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). 2 biological replicates for each sample were used. Input DNA sample corresponding to each ChIP sample was also sequenced in parallel. We have developed a native antibody for the protein (GRMZM2G014902; epitope: residues 11-77) for the ChIP-seq study.

2016-06-30 | E-GEOD-67655 | biostudies-arrayexpress

Zea mays Variation

Project description:Profiling transcription levels across many parental inbreds from the maize nested association mapping population.

2013-01-30 | E-MTAB-4328 | biostudies-arrayexpress

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize

Project description:Maize is highly sensitive to short term flooding and submergence. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18W and M162W) and sensitive (B97 and B73) genotypes were identified. Transcriptome analysis was performed on these inbreds to provide genome level insights into the molecular responses to submergence. RNA deep sequencing of shoot tissue from four inbreds (B73, B97, Mo18W and M162W) in three conditions 24h control (non-submerged), 24h submerged and 72h submerged.

2015-01-01 | E-GEOD-63429 | biostudies-arrayexpress

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Project description:We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 maize inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes in maize exceeds 103,000 and that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres further revealed the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that correlate with known QTLs and changes in gene expression.

2021-02-01 | GSE165787 | GEO

Genetic and Molecular Characterization of Submergence Response Identifies Subtol6 as a Major Submergence Tolerance Locus in Maize

2015-01-01 | GSE63429 | GEO

Transcriptome analysis of proliferative tissue of eight maize inbred lines

Project description:Genome-wide transcriptomics experiment (RNA-seq) on proliferative tissue of eight maize inbred lines (A632, B73, B96, F7, H99, HP301, Mo17, W153R). These inbreds are used as parents in a funnel breeding design to generate an advanced recombinant maize population.

2015-06-29 | E-MTAB-3173 | biostudies-arrayexpress

Project description:Expression profiling analyses for 5 maize inbreds and 4 hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10236). Keywords: Genotype comparison series

2008-02-22 | GSE10542 | GEO

CornChip0-Maize Pilot GeneChip Array

Project description:To define the parameters necessary to design short oligo arrays for maize (Zea mays L.), a species with particularly high nucleotide (SNP) and insertion-deletion (indel) polymorphism frequencies, gene expression was analyzed in for four maize inbred lines using a custom Affymetrix DNA array. Statistically significant interactions between probes and maize inbreds were detected, affecting five or more probes (out of 30 probes per transcript) in the majority of cases, indicating the effect of polymorphisms on gene expresison estimates using this platform. Keywords: genotype effect

2006-04-14 | GSE4663 | 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