Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of 103 RILs of a B73 x H99 RIL population

ABSTRACT: The RIL population used in this study is derived from a cross between parental lines B73 and H99, followed by 12 generations of self-pollination. In total 142 RILs were generated and 223 markers were used for mapping these RILs (Marino et al. (2009) Mol Genet Genomics, 281:163-179). The transcriptome of a randomly chosen subset of 103 RILs was analyzed in this study using RNA-seq.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Zea mays

SUBMITTER: Plant Systems Biology data submission

PROVIDER: E-MTAB-3758 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population.

Baute Joke J Herman Dorota D Coppens Frederik F De Block Jolien J Slabbinck Bram B Dell'Acqua Matteo M Pè Mario Enrico ME Maere Steven S Nelissen Hilde H Inzé Dirk D

Genome biology 20150911

<h4>Background</h4>To sustain the global requirements for food and renewable resources, unraveling the molecular networks underlying plant growth is becoming pivotal. Although several approaches to identify genes and networks involved in final organ size have been proven successful, our understanding remains fragmentary.<h4>Results</h4>Here, we assessed variation in 103 lines of the Zea mays B73xH99 RIL population for a set of final leaf size and whole shoot traits at the seedling stage, complem ...[more]

PMID: 26357925

Similar Datasets

Transcriptome analysis of 94 RILs of a maize MAGIC RIL population

Project description:In this study we used a maize multiparental advanced generation intercross (MAGIC) population, originating from nine parental lines (A632, B73, B96, F7, H99, HP301, Mo17, W153R and CML91) followed by 6 generations of self-pollination. A subset of 94 lines was chosen randomly from the set of 529 lines that was genotyped and phenotyped in the field (Dell'Aqua et al (2015) Genome Biology, 16:167) and sampled for RNA seq of proliferative tissue of growing leaf.

2016-02-02 | E-MTAB-3965 | biostudies-arrayexpress

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

Natural variation of gibberellin responses in Arabidopsis thaliana

Project description:To assess natural variation in the ability to respond to changes in gibberellin metabolism, we examined the effect of the ectopic expression of GA20ox1 in 10 Arabidopsis thaliana accessions. RNA-seq was performed on the sixth leaf, which was micro-dissected (size < 0.25 mm2) at the beginning of the transition from cell proliferation to cell expansion.

2017-12-14 | E-MTAB-4508 | biostudies-arrayexpress

Disrupting SUMOylation potentiates transactivation function and ameliorates polyglutamine AR-mediated disease

Project description:Our findings demonstrate beneficial effects of enhancing transactivation function of the ligand-activated polyQ AR and indicate that the SUMOylation pathway may provide new targets for therapeutic intervention. We mutated conserved lysines in the polyQ AR that are targeted by SUMO, a modification that inhibits AR transactivation function.

2015-12-21 | E-GEOD-60691 | biostudies-arrayexpress

Expression analysis of Arabidopsis seedlings 3h and 2h after transfer to sucrose

Project description:Seedlings are grown on a mesh covering MS media without carbon source, and subsequently transferred at 9 DAS to control media without sucrose or medium supplemented with 15 mM sucrose. 3 hours and 24 hours after transfer, seedlings were harvested and the third leaf micro-dissected for RNA extraction.

2017-12-14 | E-MTAB-4262 | biostudies-arrayexpress

A bioinformatics approach reveals novel mechanisms of the OVOL transcription factors in the regulation of epithelial-mesenchymal cell programming and cancer progression.

Project description:We find significant evidence of the OVOL, AP1, STAT1, STAT3, and NFKB1 TFs having important roles in MET. We prioritize known gene/drug targets for follow-up in the clinic, and show that the AP1/MYC TF pair is a strong candidate for intervention. Examination of the effects of OVOL1 and OVOL2 overexpression common to prostate cancer and breast cancer models.

2014-03-20 | E-GEOD-51975 | biostudies-arrayexpress

DUSP4 deficiency due to promoter hypermethylation drives oncogenic JNK signaling and tumor cell survival in diffuse large B-cell lymphoma

Project description:The epigenetic dysregulation of tumor suppressor genes is a major driver of human carcinogenesis. We have combined genome-wide methylation analyses with functional screening to identify novel candidate tumor suppressor genes in diffuse large B-cell lymphoma (DLBCL). We find that the dual-specificity phosphatase DUSP4 is aberrantly silenced in nodal and extranodal DLBCL due to promoter hypermethylation; ectopic expression of wild type DUSP4, but not of a phosphatase-deficient mutant, dephosphorylates c-JUN N-terminal kinase (JNK) and induces apoptosis in DLBCL cells. JNK inhibition prevents DLBCL survival in vitro and in vivo, and synergizes strongly with inhibitors of chronic active B-cell receptor signaling. Our results provide a mechanistic basis for the clinical development of JNK inhibitors in DLBCL, alone or in synthetic lethal combinations. A methylation profiling data set related to this experiment was also deposited at ArrayExpress under accession number E-MTAB-2926: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2926/

2015-03-25 | E-MTAB-2925 | biostudies-arrayexpress

Zea mays Transcriptome or Gene expression

Project description:Gene transcription is an essential step of gene function and transcriptome variation is of agronomical, ecological and evolutionary importance. To explore global expression patterns and dissect the underlying genetic mechanisms are important scientific inquires which are still largely unknown, especially between a segregating population and the parents. In our study, we used RNA-Seq to profile the shoot apex transcriptome variation (including protein coding genes and non-coding genes) in maize IBM RIL population, to map eQTLs underlying the transcriptome variations and to utilize eQTLs to clone genes involved in maize shoot apices development. We revealed that: Much of the variation (the population mean, the coefficient of variation) of gene expression levels in RILs is reflective of differences present among the parents; These transcriptome variations could be explained by 30,774 eQTLs with 96 trans-eQTL hotspots; In many cases, the genes commonly regulated by a trans-eQTL hotspot are enriched for a specific function or act in the same genetic pathway; Structural variation within and near genes contributs to cis-regulatory variation. All of these results indicate Mendelian factors play as major contributors to the transcriptome variation. Meanwhile, non-Mendelian regulations were also observed as paramutation-like expression pattern for 145 genes, of which 88% genes were predicted to be potential targets of miRNAs or ta-siRNAs, and as unexpected presence/absence expression patterns for 210 genes. These genes with unexpected presence/absence expression patterns in the RILs likely include examples of functional genes as well as transposed gene fragments that may contribute to regulatory variation of their ancestral syntenic genes.

2013-01-30 | E-MTAB-4227 | biostudies-arrayexpress

Transcriptome analysis of 103 RILs of a B73 x H99 RIL population

Project description:Transcriptome analysis of 103 RILs of a B73 x H99 RIL population

| PRJEB9918 | ENA

Multifaceted Activity of Cytokinin at Distinct Phases of Leaf Development Shapes Its Size and Structure in Arabidopsis thaliana

Project description:We performed a transcriptome profiling on the leaf 3 microdissected from plants with altered cytokinin levels 3h after activation at 9 DAS, when this leaf is normally fully composed of proliferating cells to get an insight into dynamics of molecular network underlying cell responses to CK excess and deficiency in proliferating cells. Seeds of Arabidopsis thaliana transgenic lines (CaMV35S>GR>ipt and CaMV35S>GR>HvCKX2) and corresponding wild-types (Col-0) were sown on nylon meshes placed on half-strength Murashige and Skoog (MS) medium containing 0.5% (w/v) MES and 0.8% (w/v) agar. After 2 days of stratification, plants were removed to growing chambers with 16-h day/8-h night, 21 C and 19 C, respectively, under continuous light (110 mol m-2 s-1). DEX-inducible lines and wild-types were activated at 9 DAS by transfer of nylon meshes to half-strength MS medium supplemented with either 2.5 M DEX dissolved in 5x10-4% (v/v) DMSO or just 5x10-4% (v/v) DMSO (mock). The leaf 3 was dissected from i > 250 individual seedlings per variant on a cooling plate under a stereomicroscope with precision needle and removed into the liquid nitrogen. For RNA-seq 2 biological replicates of WT, ipt and HvCKX2 activated by DEX were used. The RNA was extracted according the same method described for qRT-PCR. RNA sequencing was done by GATC Biotech AG (Konstanz, Germany).

2020-01-09 | E-MTAB-6109 | 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