GEO DataSets

(Submitter supplied) To further confirm whether the expression of NRT genes were influenced by pathogen infection, maize leaves were sampled at 0h, 24h, 40h, 60h and 96h post inoculation with wild-type strain Colletotrichum graminicola, the causing agent of maize anthracnose disease.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

15 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

Platforms:

GPL15463 GPL20156

9 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) The goals of this study are to compare NGS-derived transcriptomes (RNA-Seq) derived from ded1-ref mutant and normal maize endosperm tissue. Homozygous ded1-ref mutants exhibit a seed defect. Maize Ded1 encodes a transcription factor. This study characterizes DEGs between ded1-ref and normal endosperm and serves to identify direct target genes together with DAP-seq data.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

8 Samples

Download data: XLSX

(Submitter supplied) The goal of this study is to clarify the function of ZmTE1 in auxin signal pathway and regulting cell cycle related genes. We isolated total RNA from the three nodes together with internodes of 28-day-old B73 and ZmTE1 seedlings. New genes act downstream of ZmTE1 at the nodes, are discovered.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

6 Samples

Download data: XLS

(Submitter supplied) The maize ocl4 mutants showed differing levels of male sterility, which seems correlating with the quantity of 21-nt phasiRNA remaining during pre-meiotic stage. In this case, sRNA and transcriptome was profiled and compared in this study, showed that OCL4 and 21-nt phasiRNAs are dispensable for male fertility in maize anthers.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15463

16 Samples

Download data: TXT

(Submitter supplied) The root system is fundamental for maize growth and yield. The primary root system is the most important structure of maize seedlings and is the first organ that emerges at germination, providing water and nutrients for the growing seedlings. However, it is difficult to characterize them at single cell level, due to their complex and heterogeneous cell types. In this study, we profiled the transcriptomes of more than 7000 cells derived from maize root tips of seedlings grown on media with (nitrate+) or without nitrate (nitrate-).

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15463 GPL20156

6 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) To determine the centromere of the maize B chromosome, we used previously published anti-CENH3-ChIP-seq data from TB-9Sb, which contain a complete functional B centromere. Distribution of centromere-specific DNA repeats, including CentC, CRM element and B-repeat, were observed in the proximal end of the assembled maize B chromosome, and this region was shown to be associated with CENH3 nucleosomes. Furthermore, six small scaffolds with sizes ranging from 10 to 174 kilobase display CENH3 enrichment, also with the distribution of these repeat sequences. These results were consistent with previously cytogenetic observation. Therefore, approximately 520 kb centromeric regions were determined in the assembled maize B chromosome.

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15463

1 Sample

Download data: BEDGRAPH

(Submitter supplied) Gibberella stalk rot (GSR) caused by Fusarium graminearum is one of the devastating diseases causing significant losses to maize production worldwide. Although plant oxylipins have been widely reported as potent signals to activate diverse biotic stress responses, the roles of distinct oxylipin pathway branches initiated by either 9- or 13-lipoxygenases (LOXs) in defense against GSR remain unexplored. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

18 Samples

Download data: CSV

(Submitter supplied) The biotrophic fungal pathogen Ustilago maydis cause common smut in maize, and lead to gall formation on all aerial organs, especially on maize kernel thus reduce yield. The interaction of U. maydis with maize is a well-established model to study the interaction between maize and biotrophic pathogen. U. maydis infection could activate host immune responses including: ROS accumulation, protease activation, salicylic acid signaling. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

24 Samples

Download data: CSV

(Submitter supplied) Gibberella stalk rot (GSR) caused by Fusarium graminearum is one of the most devastating diseases causing significant yield loss of maize, and GSR resistance is a quantitative trait controlled by multiple genes. Although a few QTLs/resistance genes have been identified, the molecular mechanisms underlying GSR resistance remain largely unexplored. To identify potential resistance genes and to better understand the molecular mechanism of GSR resistance, a transcriptomic was conducted using two inbred lines with contrast GSR resistance, K09 (resistant) and A08 (susceptible) upon infection with F. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

44 Samples

Download data: CSV

(Submitter supplied) Purpose: This study is designed to identify genes and processes that are differentially regulated in corn when it is grown with or without weeds through the entire critical weed free period (to V8) or when weeds were removed early in the critical weed free period (at V4) and the plants were allowed to recover until V8. Methods: Corn was grown as described above in field plots near Brookings SD in 2007 and 2008 and RNA was extracted from the top-most leaf tips from four plants per treatment plot. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

17 Samples

Download data: CSV

(Submitter supplied) miRNAs play important roles in every aspect of plant development. Small RNA regulation confers sensitivity and robustness onto gene regulatory networks, and the morphogen-like readout of small RNA mobility gradients yields sharply delineated domains of target gene expression. However, how the spatiotemporal patterns of miRNA activity are attained is less well understood. We used the high-resolution maize shoot apex transcriptome atlas (Knauer et al., 2019) together with data from small RNA-Seq, PARE analysis, small RNA in-situ hybridization, and RNAseq of weak dcl1 mutant tissues to demonstrate that miRNA accumulation and function during development is regulated in a tiissue dependent manner at the transcriptional and post-transcriptional level.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15463 GPL17628

9 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; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL15463 GPL13977

33 Samples

Download data: TXT

(Submitter supplied) Starch synthesis is an essential feature for crops, but its regulatory mechanism has been largely restricted to transcription factors. Starch synthesis parallels the endosperm development in maize. we obtained transcriptome, small RNAome and DNA methylome data from the multiple developing stages of endosperms, as well as kernel and leaf, via applying RNA-seq, sRNA-seq and BS-seq technologies. We demonstrated that genome-wide gene expression makes a sharp transition at the point when starch accumulation speeds between DAP 10-13, while the enriched up-regulation of starch and sucrose metabolism genes occurs earlier at DAP 9-10. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

11 Samples

Download data: TXT

(Submitter supplied) Starch synthesis is an essential feature for crops, but its regulatory mechanism has been largely restricted to transcription factors. Starch synthesis parallels the endosperm development in maize. we obtained transcriptome, small RNAome and DNA methylome data from the multiple developing stages of endosperms, as well as kernel and leaf, via applying RNA-seq, sRNA-seq and BS-seq technologies. We demonstrated that genome-wide gene expression makes a sharp transition at the point when starch accumulation speeds between DAP 10-13, while the enriched up-regulation of starch and sucrose metabolism genes occurs earlier at DAP 9-10. more...

Organism:

Zea mays

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15463

11 Samples

Download data: TXT

(Submitter supplied) DNA methylation is a ubiquitous chromatin feature — in maize, more than 25% of cytosines in the genome are methylated. Recently, major progress has been made in describing the molecular mechanisms driving methylation, yet variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here we leveraged whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) on populations of modern maize, landrace, and teosinte (Zea mays ssp. more...

Organism:

Zea mays

Type:

Other; Methylation profiling by high throughput sequencing

Platforms:

GPL15463 GPL17628

74 Samples

Download data: BED, XLS

(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

Platforms:

GPL15463 GPL25410

28 Samples

Download data: WIG

(Submitter supplied) H3K27me3 usually enriched with low or no expressed genes in animal or plant genomes. However, some researches indicate that H3K27me3 can be enriched with high expressed genes in human genome. It's still unknown that whether this kind of gene is appeared in plant genomes and the mechanisms are also unclear. In this study we used ChIP-seq to develop high resolution profiles of H3K27me3 distributions in several tissues or cell-types of maize to better understand the role of this mark in an important crop. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

10 Samples

Download data: CSV

(Submitter supplied) H3K27me3 usually enriched with low or no expressed genes in animal or plant genomes. However, some researches indicate that H3K27me3 can be enriched with high expressed genes in human genome. It's still unknown that whether this kind of gene is appeared in plant genomes and the mechanisms are also unclear. In this study，we used ChIP-seq to develop high resolution profiles of H3K27me3 distributions in several tissues or cell-types of maize to better understand the role of this mark in an important crop. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL15463 GPL25410

18 Samples

Download data: WIG

(Submitter supplied) In higher plants, the outer surface of the aerial parts is covered by the cuticle, a complex lipid layer that constitutes a barrier against damages caused by environmental factors and provides protection against non-stomatal water loss. We show in this study that cuticle deposition, during the juvenile phase of in maize (Zea mays) plant development, and cuticle-dependent leaf permeability are controlled by the MYB transcription factor ZmMYB94/FUSED LEAVES1(ZmFDL1). more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

6 Samples

Download data: TXT