Inner stem tissue of V2 seedlings and husks (maize B73)
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE94254 | GEO | 2017/07/03
SECONDARY ACCESSION(S): PRJNA369198
REPOSITORIES: GEO
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Project description:Inner stem tissue of V2 seedlings and husks (maize B73)
| PRJNA369198 | ENA
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Project description:Most cells in a multicellular organism carry the same genetic information; however, they can still differentiate to take up different functions in the organism. This differentiation process involves tight regulation of gene expressions by regulatory sequences including transcriptional enhancers. Enhancers can be located distantly from their target genes; this characteristic makes it difficult to identify enhancers only using experimental approaches. Importantly, enhancers carry characteristic chromatin signatures such as low DNA methylation, high chromatin accessibility and histone modifications such as H3K9ac and H3K27ac. Computational enhancer identification approaches often use machine learning methods in combination with a number of experimental genome-wide datasets to identify key enhancers features and scans the whole genome. Limited knowledge on plant enhancers restricts us in available approaches we can use to perform genome-wide enhancer prediction in plant species. In this work, we have integrated genome-wide low DNA methylation, chromatin accessibility and H3K9ac data from two tissues, inner stem tissue (V2-IST) from seedlings at the V2 stage and husk tissue, in the crop plant Zea mays. This study identified approximately 1,400 candidate enhancers. By comparing data from two different tissues, we determined tissue-specificity of the candidate enhancers. We also have associated putative target genes using gene expression data taking an advantage of having data from two tissues.
2017-07-03 | GSE94252 | GEO
Project description:Most cells in a multicellular organism carry the same genetic information; however, they can still differentiate to take up different functions in the organism. This differentiation process involves tight regulation of gene expressions by regulatory sequences including transcriptional enhancers. Enhancers can be located distantly from their target genes; this characteristic makes it difficult to identify enhancers only using experimental approaches. Importantly, enhancers carry characteristic chromatin signatures such as low DNA methylation, high chromatin accessibility and histone modifications such as H3K9ac and H3K27ac. Computational enhancer identification approaches often use machine learning methods in combination with a number of experimental genome-wide datasets to identify key enhancers features and scans the whole genome. Limited knowledge on plant enhancers restricts us in available approaches we can use to perform genome-wide enhancer prediction in plant species. In this work, we have integrated genome-wide low DNA methylation, chromatin accessibility and H3K9ac data from two tissues, inner stem tissue (V2-IST) from seedlings at the V2 stage and husk tissue, in the crop plant Zea mays. This study identified approximately 1,400 candidate enhancers. By comparing data from two different tissues, we determined tissue-specificity of the candidate enhancers. We also have predicted putative target genes using gene expression data taking an advantage of having data from two tissues.
2017-07-03 | GSE94251 | GEO
Project description:Maize earshoot is a metabolic sink espcially related to nitrogen metabolism. Studies on the transcriptomic and metabolic changes occuring in earshoot can provide interesting answers about the nitrogen metabolic potential of the maize variety under study. B73 X Mo17 is a model maize hybrid. Developing earshoots from this genotype grown at nitrogen-deficient and nitrogen-sufficient conditions were sampled, processed and analyzed through microarray technology.
2010-01-14 | GSE17932 | GEO
Project description:Here we report genome-wide high resolution allele-specific maps of DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3) in maize endosperm. To investigate the allele-specific DNA methylation pattern of maize endosperm on a genome-wide scale, we performed MethylC-seq for shoot, embryo, and endosperm tissue 12 d after pollination (DAP) of inbred B73, and the endosperm tissue 12 DAP of reciprocal crosses B73 Ã Mo17 (BM) and Mo17 Ã B73 (MB). We also performed additional RNA-seq for samples from 12-DAP and 10-DAP endosperm of both reciprocal crosses between inbreds B73 and Mo17
2013-10-17 | E-MTAB-4206 | biostudies-arrayexpress
Project description:In this study, plants of maize inbred line B73 descended from two different sets of seed material grown for several generations either in the field or in the greenhouse were found to show a different growth phenotype and ionome under phosphate starvation conditions and moreover a different responsiveness towards mycorrhizal fungi of the species Glomus intraradices (syn: Rhizophagus irregularis).Transcriptome sequencing of three individuals from each set lent further support to the location of the introgression intervals and confirmed them to be fixed in all sequenced individuals. Moreover, we identified >120 genes differentially expressed between the two B73 lines.
2014-05-02 | E-MTAB-4285 | biostudies-arrayexpress
Project description:Maize earshoot is a metabolic sink espcially related to nitrogen metabolism. Studies on the transcriptomic and metabolic changes occuring in earshoot can provide interesting answers about the nitrogen metabolic potential of the maize variety under study. B73 X Mo17 is a model maize hybrid. Developing earshoots from this genotype grown at nitrogen-deficient and nitrogen-sufficient conditions were sampled, processed and analyzed through microarray technology. B73 X Mo17 hybrid_developing earshoot microarray data: Technical replicates, no biological replicates
2010-01-13 | E-GEOD-17932 | biostudies-arrayexpress
Project description:Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and smRNA transcriptomes in maize We report an integrated genome-wide analysis of DNA methylation, histone modifications, smRNAs and mRNA transcriptional activity, using maize as a model. We surveyed the epigenomes of the maize inbred line B73 in shoot and root tissue by Illumina/Solexa 1G parallel sequencing after digesting genomic DNA with a methylation-sensitive restriction enzyme and after conducting chromatin immunoprecipitations (ChIP) using antibodies that target specific histone modifications (H3K4me3, H3K9ac, H3K27me3, H3K36me3, respectively). Additionally, we profiled RNA pools (micro RNA (miRNA), siRNA and mRNA) using the same sequencing strategy. Keywords: Epigenetics, mRNA transcription and small RNAs H3K4me3, H3K9ac, H3K27me3, H3K36me3, DNA methylation and mRNA, small RNA profiled from shoots and roots of 14 day-old maize B73 seedlings
2009-04-27 | E-GEOD-15286 | biostudies-arrayexpress
Project description:To gain insight into the genetic and molecular mechanisms that underlie the enhanced resistance of pan1 lines to vascular spread of P. stewartii, we used RNA-seq to compare the transcriptomes of B73 and pan1 lines one day after mock or bacterial inoculation of leaf veins, being this the first analysis of maize transcriptional responses to P. stewartii infection.
2019-07-10 | GSE133303 | GEO