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E-GEOD-94252

ABSTRACT: Genome-wide gene expression profile in inner stem tissue of V2 seedlings and husks (maize B73) [RNA-Seq]

PROVIDER: E-GEOD-94252 | ExpressionAtlas | 2023-06-15

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-94252-analysis-methods.tsv	Tabular
	E-GEOD-94252-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-94252-coexpressions.tsv.gz	Tabular
	E-GEOD-94252-configuration.xml	Xml
	E-GEOD-94252-factors.xml	Xml

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Project description:Genome-wide gene expression profile in inner stem tissue of V2 seedlings and husks (maize B73) [RNA-Seq]

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RNA-seq of whole maize seedlings

Project description:RNA-seq from whole V3 maize seedlings (roots and shoots) for the B73 inbred line and A188 x B73 hybrid.

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Maize single base resolution methylome in B73 and Mo17 inbred line and their reciprocal hybrid

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

Abscisic acid transcriptional response of the maize epigenetic mutant, mop1-1

Project description:MOP1-dependent and ABA-responsive pathways act within complex, connected transcriptional regulatory networks to mediate tissue-specific growth and responses to abiotic stress in maize Purpose: To identify genome-wide ABA-induced, MOP1-dependent and independent transcriptional responses Methods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 8 hours. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR. Results: we mapped ~23 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 3,242 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a fold change ≥2 and FDR <0.05, 1,561 DEGs were found to be unique to one genotype/treatment comparison. Conclusions: Our study represents the first analysis of ABA in maize seedlings in the RdDM (mop1-1) mutant, with biological replicates, and generated by RNA-seq technology. We identified common targets of MOP1 and ABA transcriptional regulation.

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Epigenetic modifications and their relationships to smRNA and mRNA transcriptomes in maize

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

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

Inner stem tissue of V2 seedlings and husks (maize B73)

Project description:Inner stem tissue of V2 seedlings and husks (maize B73)

| PRJNA369198 | ENA

Inner stem tissue of V2 seedlings and husks (maize B73)

Project description:Genome-wide prediction of transcriptional enhancers in maize B73 using DNase-seq and H3K9ac ChIP-seq. RNA-seq data was used to associate potential target genes to enhancer candidates.

2017-07-03 | GSE94254 | GEO

Zea mays Transcriptome or Gene expression

Project description:Maize is one of the most important crops in the world and serves as an excellent model for seed development research. Despite the important role of the transcriptome in development, genome-wide expression throughout the process of maize seed development has not been characterized. Using RNA-seq, we developed a spatio-temporal transcriptome atlas of B73 maize seed development from fertilization to maturity for embryo, endosperm, and whole seed tissue.

2015-02-12 | E-MTAB-4432 | biostudies-arrayexpress

Direct and indirect transcriptional effects of abiotic stress in Zea mays plants defective in RNA-directed DNA methylation

Project description:MOP1-mediated regulation of gene expression of plant responses to early ABA induction has transcriptionally and physiologically relevant roles. Homozygous mop1-1 plants are compromised in their ability to recover from water deprivation. Purpose: Genome-wide identification of immediate and direct MOP1-dependent ABA transcriptional responses Methods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 1 hour. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR. Results: we mapped ~33 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 1,856 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a log2FC ≥ 0.95 and FDR <0.05, 1,119 DEGs were found to be unique to one genotype/treatment comparison. Conclusions: MOP1-mediated regulation of gene expression in maize seedlings in the RdDM (mop1-1) mutant has relevant transcriptional and physiological roles in plants subjected to stress. Our study generated by RNA-seq technology identified genes and biological processes regulated by RdDM and ABA-mediated stress responses, including MOP1-dependent and immediate response genes (MIMs).

2021-07-08 | GSE179629 | GEO

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