GEO DataSets

(Submitter supplied) The apoplast of host plants serves as a dynamic interface during invasion and subsequent establishment of disease by a microbial pathogen. In the recent past, host plant apoplasts have been demonstrated to harbour small membrane bound vesicles called extracellular vesicles (EVs) that contain both RNA and protein. EVs are considered to play a significant role in cell-cell communication between the host and the pathogen during infection. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL34900

36 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

43 Samples

Download data

(Submitter supplied) An understanding of how genetic variants affect chromatin accessibility in unique cellular context remains poorly understood. Here, we generated single-cell chromatin accessibility profiles in nearly 200 diverse maize inbred lines, revealing for the first time variants that affect chromatin accessibility in distinct cellular contexts.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

3 Samples

Download data: RDS, TXT

(Submitter supplied) Gene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis-regulatory activity remains limited. Here, we investigated the consequences of cis-regulatory diversity using single-cell genomics of >0.7 million nuclei across 172 maize inbreds. Our analyses pinpointed cis-regulatory elements distinct to domesticated maize and how transposons rewired the regulatory landscape. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25410

40 Samples

Download data: RDS

(Submitter supplied) A whole transcriptome (RNA-seq) study of maize root and shoots under iron sufficient, deficient and resupply conditions was carried out to determine the genes that are iron-regulated in the roots and shoots.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

18 Samples

Download data: TABULAR, TSV

(Submitter supplied) Loss-of-function mutant alleles were characterized for 22 maize transcription factors to test the functional relevance of prior yeast-one-hybrid and co-expression gene regulatory network predictions. The transcriptome and phenolic metabolome of these mutants were profiled to document the functional roles of these transcription factors. A subset of the prior gene regulatory network predictions were supported but had limited overall power in predicting changes in gene expression or phenolic compounds. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25410 GPL24163

113 Samples

Download data: TSV

(Submitter supplied) The 7d-mesocotyls of wild type B73 and its ZmWRKY53-KO counterparts were treated with or without S. reilianum for RNA sequencing.The differentially expressed genes (DEGs) were identified based on the criteria of fold-change > 2 and P < 0.05. Under normal conditions, we found 1,025 downregulated and 599 upregulated differentially expressed genes (DEGs) in the ZmWRKY53-KO plant compared to its wild-type B73 counterpart. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

12 Samples

Download data: CSV, TXT

(Submitter supplied) During a proof-of-concept study, virome of millet, grown as weed was determined by small RNA HTS. As a result, from the pools of 20 randomly collected millet samples collected at two locations, we identified the presence of three viruses, two of them first time in Hungary. Based on our results we could only suspect that these viruses: wheat streak mosaic virus (WSMV), barley stripe mosaic virus (BYSMV) and barley virus G (BVG) could have been overwintered in millet or other monocotyledonous weeds growing at these fields. more...

Organism:

Zea mays; Setaria viridis; Cynodon dactylon; Echinochloa crus-galli; Panicum miliaceum; Sorghum halepense

Type:

Other

6 related Platforms

7 Samples

Download data: TXT

(Submitter supplied) The endosperm of cereal grains feeds the entire world as major food supply, however little is known for its defense responses during endosperm development. Inducer of CBF Expression 1 (ICE1) is a known regulator of cold tolerance in plants. ICE1 has a monocot-specific homologue that is preferentially expressed in cereal grains but with an unclear regulatory function. Here, we characterized the function of monocot-specific ZmICE1 (ZmICE1a) in maize (Zea mays) kernel. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

24 Samples

Download data: TXT

(Submitter supplied) The endosperm of cereal grains feeds the entire world as major food supply, however little is known for its defense responses during endosperm development. Inducer of CBF Expression 1 (ICE1) is a known regulator of cold tolerance in plants. ICE1 has a monocot-specific homologue that is preferentially expressed in cereal grains but with an unclear regulatory function. Here, we characterized the function of monocot-specific ZmICE1 (ZmICE1a) in maize (Zea mays) kernel. more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25410

4 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) The apoplast of host plants serves as a dynamic interface during invasion and subsequent establishment of disease by a microbial pathogen. In the recent past, host plant apoplasts have been demonstrated to harbour small membrane bound vesicles called extracellular vesicles (EVs) that contain both RNA and protein. EVs are considered to play a significant role in cell-cell communication between the host and the pathogen during infection. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34900

36 Samples

Download data: GTF

(Submitter supplied) Concomitant cloning of RNA degradation products is a major issue in standard small RNA-sequencing practices. It not only adds complexity in bona fide sRNA characterization, but also affects experimental replicability and sometimes results in library construction failure. Given that all kinds of canonical plant small RNAs bearing the 3’ end 2’-O-methylation modification, we here developed an sRNA-seq method (named terminal ribose-modified sRNA sequencing, TRM-sRNA-seq).

Organism:

Oryza sativa; Arabidopsis thaliana; Solanum lycopersicum; Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

54 Samples

Download data: TXT

(Submitter supplied) Some pathogen-derived effectors reprogram mRNA splicing in their host plant to regulate plant immune responses. The fungus Exserohilum turcicum is the causal agent of northern corn leaf blight, a damaging maize (Zea mays) disease. However, the low efficiency of genetic transformation of E. turcicum has hampered research on its effectors and whether E. turcicum effectors interfere with RNA splicing remained unknown. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

27 Samples

Download data: TXT

(Submitter supplied) In the study, RBSDV accumulation was detected in NIL-S starting from 16 days post inoculation (dpi) and increased linearly thereafter to reach a high level. Concurrently, the viral S10 encoding the coat protein exhibited a dramatic accumulation in NIL-S but not in NIL-R, as did the viral S7-1. We performed RNA-seq analysis at 16 dpi between NIL-S and NIL-R. The differentially expressed genes (DEGs) were identified based on the criteria of fold-change > 2 and P < 0.05. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

4 Samples

Download data: XLS

(Submitter supplied) The maize inbred lines Chang7-2 (resistant to SCMV) and Mo17 (susceptible to SCMV) were inoculated with SCMV (SC, SM) and phosphate buffer (MC, MM), respectively to subjected to degradome sequencing.

Organism:

Zea mays

Type:

Other

Platform:

GPL17628

1 Sample

Download data: XLSX

(Submitter supplied) The maize inbred lines Chang7-2 (resistant to SCMV) and Mo17 (susceptible to SCMV) were inoculated with SCMV (SC, SM) and phosphate buffer (MC, MM), respectively to subjected to whole-transcriptome RNA sequencing and degradome sequencing.

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:

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:

GPL24631 GPL25410 GPL28862

54 Samples

Download data: TXT