GEO DataSets

(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) 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) 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) 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) 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) 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) NKD1, 2 and O2 are key transcription factors interactively regulating endosperm development. Their mutation combinations may diversely alter the global gene regulatory landscape. To investigate how interactions between NKD1, 2 and O2 affect endosperm regulatome, which is indicated by accessible regions for regulators on chromatins, Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed for 16 DAP endosperms of all 8 genotype combinations (2 biological replicate per genotype). more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25410

16 Samples

Download data: BW

(Submitter supplied) Transcription factors (TFs) play an important role in maize endosperm development regulation. The temporal RNA-seq and co-expression network analysis of maize endosperm reveals a hiararchical regulatory network architechture modulating the endosperm development. In the network, NKD1 and NKD2 are central regulators, and GBF1, HSFTF10, NACTF49 and HB115 are secondary regulators downstream of NKD1 and 2. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20156 GPL25410

6 Samples

Download data: NARROWPEAK

(Submitter supplied) The transcriptomic analysis of nkd1, nkd2 and o2 homozygous mutant set (including 1 WT, 3 single mutants, 3 double mutants and 1 triple mutant) at 8, 12 and 16 DAP revealed temporal regulatory landscape in endosperm grain-filling stage. The data also showed NKD1, NKD2 and O2 interactively regulate gene network overtime in several processes, such as hormone response, cell wall organization, nutrient storage and endoreduplication, etc.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

96 Samples

Download data: TSV

(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) In angiosperms, the endosperm provides nutrients for embryogenesis or seed germination and is the primary tissue where gene imprinting occurs. To map the imprintome of the early developing endosperm in maize, we performed high-throughput transcriptome sequencing of the kernels at 0, 3, 5 days after pollination (DAP) and the endosperms at 7, 10, and 15 DAP produced from the B73 and Mo17 reciprocal crosses. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

12 Samples

Download data: TXT

(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) Purpose: Analysis of gene expression level. Methods: Retinal mRNA profiles of 7 DAP endosperm of the wild-type (WT) and NF-YC11 knockout mutant were generated by deep sequencing, in triplicate, using Illumina 2000.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13834

6 Samples

Download data: XLSX

(Submitter supplied) Rice NF-YC11 is a transcription factor that plays a key regulatory role in storage substance accumulation during rice grain filling. To reveal the transcription regulatory network of NF-YC11 in rice, we performed genome-wide identification of NF-YC11 targets by immunoprecipitation sequencing (ChIP-seq) analyses in the NF-YC11-overexpression plants.

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13834

2 Samples

Download data: BED, BW, XLSX

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

Organism:

Oryza sativa

Type:

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

Platform:

GPL19290

6 Samples

Download data

(Submitter supplied) OsNF-YB1 is a transcription factor that plays important roles during rice grain filling. OsNF-YB1 is specifically expressed in aleurone layer of developing endosperm and OsNF-YB1 RNAi lines showed retardation in grain filling and produced small grains with chalky endosperm as well as the altered starch quality. To reveal the transcriptional regulatory framework of OsNF-YB1, we determined OsNF-YB1 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19290

4 Samples

Download data: BED, TXT

(Submitter supplied) Analysis of gene expression level. The hypothesis tested in the present study was that OsNF-YB1 is specifically expressed in aleurone layer of developing endosperm and suppressed expression of OsNF-YB1 results in a reduced grain-filling rate and small grains. Of the down-regulated genes, the enrichment of transmembrane transport and ATP biosynthetic process is consistent with the decreased grain-filling rate.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

2 Samples

Download data: FPKM_TRACKING