GEO DataSets

(Submitter supplied) Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds, but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we determined O2 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15463

2 Samples

Download data: BED, TXT

(Submitter supplied) Analysis of gene expression level. The hypothesis tested in the present study was that opaque2 mutant influence the expression of storage proteins. Results provide important information of the gene expression level regulation of storage proteins and other biological processes.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

2 Samples

Download data: TXT

(Submitter supplied) Analysis of gene expression level. The hypothesis tested in the present study was that zmbzip22 mutant affects nutrient metabolism and stress response.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

6 Samples

Download data: XLSX

(Submitter supplied) A new factor binds to the 27-kD γ-zein gene promoter was identified through probe affinity purification and mass spectrometry analysis. This new factor belongs to bZIP type TF (hence named as ZmbZIP22). Chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq) analysis with two biological replicates was performed to determine the DNA binding targets of ZmbZIP22. ChIP-Seq analysis detected 1,550 DNA binding sites distributed over 514 genes. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17628

4 Samples

Download data: BED, TXT

(Submitter supplied) Opaque11 (O11) is a bHLH transcription factor that plays important roles in maize endosperm development, nutrient metabolism, and stress response.

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17628

4 Samples

Download data: BED, TXT

(Submitter supplied) Analysis of gene expression level. The hypothesis tested in the present study was that o11 mutant affects nutrient metabolism and stress response.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

6 Samples

Download data: TXT

(Submitter supplied) The goals of this study are to study the regulatory network of the two maize endosperm-specific transcription factors O2 and PBF by 16-DAP endosperm transcriptome profiling (RNA-seq) of their mutants and wild type. The results utilize the expression pattern of global genes regulated by PBF and O2 to elucidate their control for storage compounds synthesis in maize kernels.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

12 Samples

Download data: TXT

(Submitter supplied) Development of the cereal endosperm involves cell differentiation processes that enable nutrient uptake from the maternal plant, accumulation of storage products and their utilization during germination. However, little is known about the regulatory mechanisms that link cell differentiation processes with those controlling storage product synthesis and deposition, including the activation of zein genes by the maize (Zea mays) bZIP transcription factor Opaque-2 (O2). more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17628

10 Samples

Download data: BED, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL19041 GPL19042

34 Samples

Download data: PAIR

(Submitter supplied) The eukaryotic nuclear genome is organized into the fundamental units of chromatin, nucleosomes. The positions and biochemical states of nucleosomes on DNA can regulate protein-DNA interactions, and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in nucleosome position relate to changes in gene expression is poorly understood. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL19042

24 Samples

Download data: PAIR, TSV

(Submitter supplied) The eukaryotic nuclear genome is organized into the fundamental units of chromatin, nucleosomes. The positions and biochemical states of nucleosomes on DNA can regulate protein-DNA interactions, and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in nucleosome position relate to changes in gene expression is poorly understood. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL19041

10 Samples

Download data: PAIR, TSV

(Submitter supplied) Epigenetic modification plays important roles in plant and animal development. DNA methylation can impact the transposable element (TE) silencing, gene imprinting and regulate gene expression.Through a genome-wide analysis, DNA methylation peaks were respectively characterized and mapped in maize embryo and endosperm genome. Distinct methylation level across maize embryo and endosperm was observed. The maize embryo genome contained more DNA methylation peaks than endosperm. However, the endosperm chloroplast genome contained more DNA methylation peaks to compare with the embryo chloroplast genome. DNA methylation regions were characterized and mapped in genome. More CG island (CGI) shore are methylated than CGI in maize suggested that DNA methylation level is not positively correlated with CpG density. The DNA methylation occurred more frequently in the promoter sequence and transcriptional termination region (TTR) than other regions of the genes. The result showed that 99% TEs we characterized are methylated in maize embryo, but some (34.8%) of them are not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated two regions between embryo and endosperm are High CpG content promoters (HCPs) and high CpG content TTRs (HCTTRs). DNA methylation peaks distinction of mitochondria and chloroplast DNA were less than the nucleus DNA. Our results indicated that DNA methylation is associated with the gene silencing or gene activation in maize endosperm and embryo. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 17 endosperm-specific expressed imprinting genes were hypomethylated in endosperm and were hypermethylated in embryo. The expression of a maize DEMETER -like (DME-like) gene and MBD101 gene (MBD4 homolog) which direct bulk genome DNA demethylation were higher in endosperm than in embryo. These two genes may be associated with the distinct methylation level across maize embryo and endosperm.The methylomes of maize embryo and endosperm was obtained by MeDIP-seq method. The global mapping of maize embryo and endosperm methylation in this study broadened our knowledge of DNA methylation patterns in maize genome, and provided useful information for future studies on maize seed development and regulation of metabolic pathways in different seed tissues.

Organism:

Zea mays

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15463

2 Samples

Download data: BED

(Submitter supplied) Background The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

21 Samples

Download data: TXT

(Submitter supplied) Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. more...

Organism:

Eucalyptus grandis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20030

5 Samples

Download data: BEDGRAPH

(Submitter supplied) We report the transcriptome profile of the developing maize endosperm of nacRNAi. The nacRNAi is the transgenic maize which knocks down the expression of both ZmNAC128 and ZmNAC130 in the developing endosperm.ZmNAC128 and ZmNAC130 are the two maize endosperm-specific NAC-type transcription factors. This study finds that nacRNAi has a broad effect on the accumulation of starch and protein by regulating their main synthetic genes.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

6 Samples

Download data: TXT

(Submitter supplied) The objective of the current study is to unravel the gene regulatory networks controlled by the nkd genes during maize endosperm developent. We compared wild type (B73) vs. nkd mutant (introgressed into B73 background) transcriptomes in aleurone vs. starchy endosperm cell types captured by laser capture microdissection technology.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

12 Samples

Download data: TXT

(Submitter supplied) Plants have developed complex mechanisms to respond and adapt to abiotic stresses, coupling elaborate modulation of gene expression together with the preservation of genome stability. Epigenetic mechanisms - DNA methylation, chromatin modifications and non coding RNAs - were shown to play a fundamental role in stress-induced gene regulation and may also result in genome destabilization, with the activation and/or the transcription of silenced transposons and retroelements, causing genome rearrangements and novel gene expression patterns. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

32 Samples

Download data: GTF, TXT

(Submitter supplied) Endogenous small RNAs (sRNAs) contribute to gene regulation and genome homeostasis but their activities and functions are incompletely known. The maize genome has a high number of transposable elements (TEs; almost 85%), some of which spawn abundant sRNAs. We performed sRNA and total RNA sequencing from control and abiotically stressed B73 wild-type (wt) plants and rmr6-1 mutants. RMR6 encodes the largest subunit of the RNA polymerase IV (Pol IV) complex, and is responsible for accumulation of most 24 nucleotide (nt) small interfering RNA (siRNAs). more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15463

50 Samples

Download data: TXT

(Submitter supplied) As maize (Zea mays) plants undergo vegetative phase change from juvenile to adult, they both exhibit heteroblasty, an abrupt change in patterns of leaf morphogenesis, and gain the ability to produce flowers. Both processes are under the control of microRNA 156, whose levels decline at the end of the juvenile phase. Gain of ability to flower is conferred by expression of miR156 targets that encode Squamosa Promoter-Binding (SBP) transcription factors, which when derepressed in the adult phase induce the expression of MADS-box transcription factors that promote maturation and flowering. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL21058

13 Samples

Download data: PAIR

(Submitter supplied) In order to dissect the gene regulatory network during the functional transition of cotyledons from non-photosynthetic storage tissue to metabolically active photosynthetic tissue, we constructed ChIP-Seq libraries for NAC and YABBY transcription factors using pooled cotyledons from seedling developmental stage 4 and stage 5. Millions of raw reads obtained from ChIP-Seq libraries were aligned to the reference soybean genome using the ultrafast Bowtie aligner to obtain quantitative data for genome matched reads. more...

Organism:

Glycine max

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15008

2 Samples

Download data: TXT