GEO DataSets

(Submitter supplied) Grain filling in maize (Zea mays L.) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1,744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. more...

Organism:

Zea mays

Type:

Other

Platform:

GPL25410

4 Samples

Download data: BED, BW

(Submitter supplied) Grain filling in maize (Zea mays L.) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1,744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

12 Samples

Download data: TXT

(Submitter supplied) Grain filling in maize (Zea mays L.) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1,744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25410

8 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Maize develops separate ear and tassel inflorescences with initially similar morphology but finally different architecture and sexuality. The detailed regulatory mechanisms underlying these changes still remain largely clear. In this study, through analyzing the time-course meristem transcriptomes and floret single-cell transcriptomes of ear and tassel we revealed the regulatory dynamics and pathways underlying inflorescence development and sex differentiation. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28862 GPL24631 GPL25410

54 Samples

Download data: TXT

(Submitter supplied) The quiescent center (QC) stem cells of maize (Zea mays L.) roots are highly hypoxic under normal oxygen tension. Despite this state, they are vulnerable to hypoxic stress which causes their degradation with the subsequent inhibition of root growth. These effects are abolished by over-ever-expression of the nitric oxide (NO) scavenger Phytoglobin 1 (ZmPgb1.1) preserving the functionality of the QC stem cells during the stress. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

18 Samples

Download data: CSV

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

Organism:

Citrus sinensis; Zea mays; Brassica napus; Glycine max; Populus; Solanum tuberosum; Oryza sativa; Saccharum officinarum; Dianthus caryophyllus; Arabidopsis thaliana; Solanum lycopersicum

Type:

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

11 related Platforms

160 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. more...

Organism:

Dianthus caryophyllus; Solanum lycopersicum; Zea mays; Arabidopsis thaliana; Brassica napus; Solanum tuberosum; Saccharum officinarum; Citrus sinensis; Populus; Oryza sativa; Glycine max

Type:

Genome binding/occupancy profiling by high throughput sequencing

11 related Platforms

152 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) The goals of this study are to investigate the effect of ZMET2 on genome-wide DNA methylation and gene expression.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL25410

22 Samples

Download data: BW, TAB, TXT

(Submitter supplied) Zebra leaf is a special phenotype of variegated leaf in monocotyledonous plant. Here, we characterized a mutant zebra10 (zb10) in maize, which displays defective chloroplast development in white section of leaves at the seedling stage and pale-white kernels. Map based cloning revealed that ZB10 encodes plastid terminal oxidase (ZmPTOX) which is localized in chloroplasts. ZmPTOX protein is highest expressed in leaves and also highly expressed in endosperm. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

21 Samples

Download data: TXT

(Submitter supplied) High temperature is increasingly becoming one of the prominent environmental factors affecting the growth and development of maize (Zea mays L.). Therefore, it is critical to identify key genes and pathways related to heat stress (HS) tolerance in maize. Here, we identified a heat-resistant (Z58D) and heat-sensitive (AF171) maize inbred lines at seedling stage. Transcriptomic analysis identified 3,006 differentially expressed genes (DEGs) in AF171 and 4,273 DEGs in Z58D under HS treatments, respectively. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

8 Samples

Download data: TXT

(Submitter supplied) Fertile pollen is critical for the survival, fitness and dispersal of flowering plants, and directly contributes to crop productivity. Extensive mutational screening studies have been carried out to dissect the genetic regulatory network determining pollen fertility, but we still lack fundamental knowledge about whether and how pollen fertility is controlled in natural populations. We used a genome-wide association study (GWAS) to show that ZmGEN1A and ZmMSH7, two DNA repair-related genes, confer natural variation in maize pollen fertility. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

12 Samples

Download data: TXT

(Submitter supplied) The biochemistry of C4 photosynthesis relies on a specific suite of leaf functional properties, often referred to as Kranz anatomy, where there is increased vein density and the proportion of bundle sheath cells surrounding the veins compared to C3 photosynthesizing species. From a suite of putative Kranz anatomy regulators, TML was identified. Loss of function tml mutations lead to the development of large lateral veins in positions normally occupied by smaller intermediate veins in both C3 and C4 species tested. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

12 Samples

Download data: TXT

(Submitter supplied) The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. We demonstrate a streamlined ATAC-seq protocol for maize in which nuclei purification can be achieved without cell sorting, and using only a standard bench-top centrifuge. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25410

6 Samples

Download data: BW

(Submitter supplied) Maize husk leaf - the outer leafy layers covering the ear - modulates kernel yield and quality. Despite its importance, however, the genetic controls underlying husk leaf development remain elusive. Our previous genome-wide association study identified a single nucleotide polymorphism located in the gene RHW1 (Regulator of Husk leaf Width) that is significantly associated with husk leaf-width diversity in maize. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

6 Samples

Download data: TXT

(Submitter supplied) ngs2021_19_rhizophagus-responses of maize to the arbuscular fungus rhizophagus irregularis mitigate n deficiency stress-What is the impact of Rhizophagus irregularis on maize transcriptome under different N nutrition conditions, what is the impact of N on R. irregularis transcriptome in maize roots.-After 4 days of germination, maize seeds were sown in pots filled with sterile mix 1:1 clay beads:unfertilized peat. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

48 Samples

Download data: TXT

(Submitter supplied) Analysis of differential gene expression regulated by UVB. The hypothesis tested in the present study was that ZmUVR8 mediates mostly UVB regulated genes' expression

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

12 Samples

Download data: XLSX

(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) 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

(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

10 Samples

Download data: TXT