GEO DataSets

(Submitter supplied) This study compared the molecular basis underlying the differential regulation of p1 alleles/epialleles by mop1 to understand molecular mechanism maintaining the tissue specific silencing.

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15463

5 Samples

Download data: TXT

(Submitter supplied) MOP1-dependent and ABA-responsive pathways act within complex, connected transcriptional regulatory networks to mediate tissue-specific growth and responses to abiotic stress in maize Purpose: To identify genome-wide ABA-induced, MOP1-dependent and independent transcriptional responses Methods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 8 hours. more...

Organism:

Zea mays

Type:

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

Platforms:

GPL25842 GPL17628

17 Samples

Download data: CSV, TSV

(Submitter supplied) Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9361

3 Samples

Download data

(Submitter supplied) Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. Recent work has demonstrated that the maize MEDIATOR OF PARAMUTATION1 (mop1) gene is a predicted ortholog of the Arabidopsis RDR2 gene. The mop1 gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. more...

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL7071

2 Samples

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(Submitter supplied) MOP1-mediated regulation of gene expression of plant responses to early ABA induction has transcriptionally and physiologically relevant roles. Homozygous mop1-1 plants are compromised in their ability to recover from water deprivation. Purpose: Genome-wide identification of immediate and direct MOP1-dependent ABA transcriptional responses Methods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 1 hour. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25410

12 Samples

Download data: CSV

(Submitter supplied) To determine which of the genes differentially expressed between P1-rr and P1-ww pericarps were immediate (direct) targets of P1, we conducted chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) using P1 polyclonal antibodies (alphaP1344) that recognize the non-conserved C-terminal region of P1 (Falcone Ferreyra et al., 2010), on pericarp chromatin.

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13977

4 Samples

Download data: BED

(Submitter supplied) P1 encodes an R2R3-MYB transcription factor responsible for the accumulation of insecticidal flavones in maize silks and red phlobaphene pigments in pericarps and other floral tissues, which contributed to making P1 an important visual marker since the dawn of modern genetics. We conducted RNA-Seq using from maize silks obtained at 2-3 days after emergence. High-throughput sequencing using the Illumina platform resulted in the generation of ~14 million high quality reads, corresponding to ~7 million reads for each sample, from which 76% aligned to the maize genome.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9361

2 Samples

Download data: DIFF, FPKM_TRACKING

(Submitter supplied) P1 encodes an R2R3-MYB transcription factor responsible for the accumulation of insecticidal flavones in maize silks and red phlobaphene pigments in pericarps and other floral tissues, which contributed to making P1 an important visual marker since the dawn of modern genetics. We conducted RNA-Seq using pericarps at two different stages, 14 and 25 days after pollination (DAP). High-throughput sequencing using the Illumina platform resulted in the generation of ~20 million high quality reads, from which ~90% aligned to the recently completed maize genome sequence corresponding to ~5 million reads for each one of the four samples.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9361

4 Samples

Download data: DIFF, FPKM_TRACKING

(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:

Zea mays

Type:

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

Platforms:

GPL24163 GPL25410

44 Samples

Download data: TXT

(Submitter supplied) To determine the causes of changes in methylation during hybridization, we investigated small RNAs, particularly 24 nt small interferring RNAs (siRNAs) at the differentially methylated regions. We compared the small RNA expression between two parents (B73 and Mo17), between parents and wild type F1 (WTF1), and between WTF1 and mop1 mutant F1 (mop1F1).

Organism:

Zea mays

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24163 GPL25410

8 Samples

Download data: TXT

(Submitter supplied) To investigate how differentially methylated regions affect the flanking gene expression, we compared the gene epression between two parents (B73 and Mo17), between parents and wild type F1 (WTF1), and between WTF1 and mop1 mutant F1 (mop1F1).

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25410 GPL24163

8 Samples

Download data: TXT

(Submitter supplied) To understand the initiation of DNA methylation and its effects on gene expression, we performed high-throughput sequencing of DNA methylomes of F1 hybrids that were mutant for two genes, Mop1 (mediator of paramutation1) and Lbl1 (leafbladeless1), and their wild type F1 siblings as well as their parents. We first compared the methylation between the two parents (B73 and Mo17), and identified the differentially methylated regions (DMRs) between them. more...

Organism:

Zea mays

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL24163 GPL25410

28 Samples

Download data: TXT

(Submitter supplied) DNA methylation plays a crucial role in suppressing mobilization of transposable elements and regulation of gene expression. A number of studies have indicated that DNA methylation pathways and patterns exhibit distinct properties in different species, including Arabidopsis, rice, and maize. Here, we characterized the function of DDM1 in regulating genome-wide DNA methylation in maize. Two homologs of ZmDDM1 are abundantly expressed in the embryo and their simultaneous disruption caused embryo lethality with abnormalities in cell proliferation from the early stage of kernel development. more...

Organism:

Zea mays

Type:

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

Platform:

GPL17628

8 Samples

Download data: BED, TXT

(Submitter supplied) Transcriptional analysis of the Ufo1-1 mutant allele and wild type plants were used to identify the candidate gene using a k-mer based approach. The transcriptome data also revealed the altered expression of carbohydrate metabolic genes, which translates into elevated levels of soluble sugars in leaves and light-induced lesions found in mature Ufo1-1 leaves.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

33 Samples

Download data: TXT

(Submitter supplied) Background: Maize (Zea Mays) is an important model crop for transgenic studies. However, genetic transformation of maize requires embryonic calli derived from immature embryo, and the impact of utilizing tissue culture methods on the maize epigenome is poorly understood. Here, we generated whole-genome MeDIP-seq data examining DNA methylation in dedifferentiated and normal immature maize embryos. Results: We observed that most of the dedifferentiated embryos exhibited a methylation increase compared to normal embryos. more...

Organism:

Zea mays

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15463

12 Samples

Download data: TAR

(Submitter supplied) The contribution of epigenetic alterations to natural variation for gene transcription levels remains unclear. In this study, we investigated the functional targets of the maize chromomethylase ZMET2 in multiple inbred lines to determine whether epigenetic changes conditioned by this chromomethylase are conserved or variable within the species. Gene expression microarrays were hybridized with RNA samples from the inbred lines B73 and Mo17, and from near-isogenic derivatives containing the loss-of-function allele zmet2-m1. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL4032

18 Samples

Download data: CEL, CHP

(Submitter supplied) Using MethylC-Seq to provide single-base resolution of DNA methylation status in nrpd1-3, nrpd1-12, and nrpe1-11 mutants

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

3 Samples

Download data: WIG

(Submitter supplied) Using MethylC-Seq to provide single-base resolution of DNA methylation status in ros1-13 mutant

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17639

1 Sample

Download data: WIG

(Submitter supplied) Using MethylC-Seq to provide single-base resolution of DNA methylation status in Col-0 WT

Organism:

Arabidopsis thaliana

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13222

1 Sample

Download data: WIG