GEO DataSets

(Submitter supplied) Transcriptomics at maize embryo/endosperm interfaces identifies a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS)

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

24 Samples

Download data: TXT

(Submitter supplied) Endosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the gene regulatory networks that control endosperm cell differentiation remain largely unclear. As a first step toward characterizing these networks, we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the kernel. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

22 Samples

Download data: TXT

(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) We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. more...

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13160

13 Samples

Download data: TXT

(Submitter supplied) We used microarrays to detail the global programme of gene expression underlying cellularization and identified distinct classes of regulated genes during this process.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

2 Samples

Download data: CEL, CHP

(Submitter supplied) The receptor-like kinases (RLKs) plays critical roles in signal transduction through sensing the extracellular signals and activating the downstream signal transduction by phosphorylating their targets. Up to now, there are only a few RLKs have been functionally identified. In this study, we systemically analyzed the expression pattern of rice genes, especially the RLK coding genes during embryo and endosperm development.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

14 Samples

Download data: CEL

(Submitter supplied) Expression profiles of protein coding genes were characterized using Affymetrix rice genome array to compare with expression profiles of miRNAs. Keywords: tissue

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

10 Samples

Download data: CEL

(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) Endosperm is a filial structure resulting from a second fertilization event in angiosperms. As an absorptive storage organ, endosperm plays an essential role in support of embryo development or seedling germination. The accumulation of carbohydrate and protein storage products in cereal endosperm provides humanity with a major portion of its food, feed and renewal resources. However, little is known regarding the regulatory gene networks controlling endosperm proliferation and differentiation. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18179

9 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) 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) 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) Despite much knowledge is well-known on the transcriptional and enzymological regulation of many genes in starch synthesis, including SBEⅡb, Waxy, and SUS-SH1 genes, less information is available on their expression profiles as a consequence of their dysfunction. Hence, transcriptional adjustments in response to mutations were required for a better understanding of starch biosynthesis pathway, others metabolism and cell response. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL4032

9 Samples

Download data: CEL

(Submitter supplied) The embryo is responsible for transmitting genetic information to the next generation. However, the underlying gene expression and gene imprinting during early embryo development remain largely elusive in maize. Using high-throughput RNA sequencing, we analyzed the allelic gene expression patterns of maize embryos from reciprocal crosses between inbred lines B73 and Mo17 at six time points (3 to 13 days after pollination). more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

48 Samples

Download data: XLS

(Submitter supplied) The thk1 mutant, causing multiple aleurone layers, disrupts the NOT1 scaffolding subunit of the CCR4-NOT regulatory complex and dysregulates genes involved in cell division, signaling, differentiation and metabolism.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

9 Samples

Download data: TSV

(Submitter supplied) In the current study a microarray (46k, University of Arizona, USA) analysis of 21 European maize (Zea mays L.) parental inbred lines (14 dent and 7 flint) was applied. The aim was the identification of parental genes which expression levels are correlated to heterosis and/or hybrid performance for grain yield (GY) and grain dry matter content (GDMC) in the hybrid progeny (F1). Therefore gene expression profiles of differentially expressed genes of the parental inbred lines at the seedling stage were correlated with GY- and GDMC-field data of 98 flint x dent factorial crosses gained at six different locations in Germany. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL6438

63 Samples

Download data: GPR

(Submitter supplied) The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25410

49 Samples

Download data: BED, BW

(Submitter supplied) The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

18 Samples

Download data: TXT

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

Organism:

Zea mays

Type:

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

Platform:

GPL25410

196 Samples

Download data: BED, BW, MTX, NARROWPEAK, TSV, TXT

(Submitter supplied) The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25410

115 Samples

Download data: BW, NARROWPEAK