GEO DataSets

(Submitter supplied) In monocarpic plants, after the production of a certain number of fruits/seeds, the activity of the Shoot Apical Meristem (SAM) and of the meristems of the secondary axes stop in a coordinated way, leading to the cessation of flower production. This phenomenon has been called Proliferative Arrest (PA). It can be assumed as a general phenomenon in monocarpic plants, as it has been described in different species of this economically important group of plants. more...

Organism:

Pisum sativum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32857

16 Samples

Download data: TSV

(Submitter supplied) Seed quality traits of oilseed rape, Brassica napus (B. napus), exhibit quantitative inheritance determined by its genetic makeup and the environment via the mediation of a complex genetic architecture of hundreds to thousands of genes. Thus, instead of single gene analysis, network-based systems genomics and genetics approaches that combine genotype, phenotype, and molecular phenotypes offer a promising alternative to uncover this complex genetic architecture. more...

Organism:

Brassica napus

Type:

Expression profiling by array

Platform:

GPL15739

200 Samples

Download data: GPR

(Submitter supplied) The goal of this study is to clarify the function of LBD29 and MYB2 in the pathway of lateral root development. We isolated total RNA from the roots of 8-day-old Col-0 and sevaral transgene seedlings. New genes act downstream of LBD29 and MYB2, during the lateral root formation, are discovered.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: CSV

(Submitter supplied) Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the Poly(A) signal (PAS genes) in Arabidopsis (Arabidopsis thaliana). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

9 Samples

Download data: SF

(Submitter supplied) The Arabidopsis genome contains two highly homologous DSS1 genes, AtDSS1(I) and AtDSS1(V). This study was designed to identify the functional differences between AtDSS1s, focusing on their potential roles in oxidative stress. We generated single dss1(I) and dss1(V) mutant lines of both Arabidopsis DSS1 genes using CRISPR/Cas9 technology. The sensitivity of homozygous mutant lines with large indels (dss1(I)del25 and dss1(V)ins18) were analyzed to oxidative stress. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

3 Samples

Download data: XLS, XLSX

(Submitter supplied) Maize is a staple food, feed, and industrial crop. Heat stress (HS) is one of the major stresses affecting maize production and is usually accompanied by other stresses, such as drought. Our previous study identified a heterotrimer complex, ZmNF-YA1-YB16-YC17, in maize. ZmNF-YA1 and ZmNF-YB16 were positive regulators of the drought stress response and were involved in maize root development. In this study, we investigated whether ZmNF-YA1 confers HS tolerance in maize. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28862

18 Samples

Download data: TXT

(Submitter supplied) Using RNA-seq to study the DEGs of the root treated with or without Fo10 under Cd

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

6 Samples

Download data: CSV

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

Organism:

Phaseolus vulgaris; Xanthomonas citri pv. fuscans

Type:

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

Platform:

GPL33255

17 Samples

Download data: SF

(Submitter supplied) Purpose: To study the differential gene expression by comparing resistant and susceptible rice cultivars against the rice blast fungus M. Oryzae. Methods: Rice leaves were collected after M. Oryzae (MO36) infection from resistant and susceptible cultivars, preserved on deep freezer on -80O C frozen on liquid nitrogen, Total RNA from rice plant tissues was extracted using RNeasy Plant Mini Kit (Qiagen) by following manufacturer protocol. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21087

4 Samples

Download data: TXT

(Submitter supplied) In the canonical RdDM, small interfering RNAs (siRNAs) are produced through the slicer activity of DICER-LIKE 3 (DCL3). Here, we describe the Arabidopsis thaliana prors1 (LUC) transgenic system in which transcriptional gene silencing (TGS) through RdDM is independent of DLC3. To identify players in the DCL3-independent pathway, a forward genetics screen was performed with the prors1 (LUC) system to identify suppressor mutants in which TGS is released. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

9 Samples

Download data: XLSX

(Submitter supplied) For the RNA-seq experiments, two-week-old seedlings were cutting and harvested the basal ends of stem cuttings (0.5 cm). Samples were collected from two biological replicates (40 cuttings each).

Organism:

Populus ussuriensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25374

2 Samples

Download data: TXT

(Submitter supplied) Arabidopsis uracil phosphoribosyltransferase (UPP) is an essential enzyme and plants lacking this enzyme are strongly compromised in chloroplast function. Our analysis of UPP amiRNA mutants has confirmed that this vital function is crucial to establish a fully functional photosynthesis as the RIESKE iron sulfur protein (PetC) is almost absent, leading to a block in photosynthetic electron transport. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

12 Samples

Download data: TXT

(Submitter supplied) The mechanism underlying CUC genes regulating leaf marginal patterning remains largely unknown. To this end, we employed MOBE-ChIP-seq to identify the downstream regulating genes of ChCUC1. The aim of this project is to map genome-wide binding sites of ChCUC1 gene .

Organism:

Cardamine hirsuta

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33698

12 Samples

Download data: BIGWIG, NARROWPEAK, TXT

(Submitter supplied) The mechanism underlying CUC genes regulating leaf marginal patterning remains largely unknown. To this end, we employed DAP-seq to identify the downstream regulating genes of ChCUC1. The aim of this project is to map genome-wide CUC genes binding sites.

Organism:

Cardamine hirsuta

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33698

6 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) Here we investigate the function of CUC1(CUP-SHAPED COTYLEDON1) in the diversification of leaf forms between simple-leaved Arabidopsis thaliana and compound-leaved Cardamine hirsuta. CUC transcription factors are conserved regulators in leaf margin dissection and leaflet formation. ChCUC1, ChCUC2 and ChCUC3 function redundantly and are required for the leaflet formation in C. hirsuta. Recently we discovered that ChCUC1 has species species-specific expression in young leaves of C.hirsuta. more...

Organism:

Cardamine hirsuta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25198

24 Samples

Download data: TXT

(Submitter supplied) Osteoporosis, the leading cause of death among older people, is characterized by low bone mineral density (BMD) and reduced bone strength. Here, we report that miR162a, a Lycium chinense Mill-encoded microRNA, directly targets bone marrow and inhibits osteoporosis. MiR162a is stable in mice’s stomach and synthetic miR162a agomir could pass through mouse Gastrointestinal tract (GI) tract and enter the sera, bone marrow and organs.

Organism:

Lycium chinense; Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24247 GPL33413

2 Samples

Download data: FA, TSV

(Submitter supplied) The histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plant genome, which could eThe histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plant genome, which could enhance gene transcription involved in stress-responsive gene expression. The physiological and molecular mechanisms underlying plant responses to insects are being increasingly studied, while epigenetic modifications such as histone acetylation and their potential regulation at the genomic level of transcription of hidden genes in plants damaged by insects remain largely unknown. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27660

6 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) In cereal crop plants, sexual development and reproduction are key steps in producing seeds. However, genes responsible for reproductive function and development are largely unknown in soybean. Here, the soybean flower development was divided into three stages, namely the early stage(E), before pollination (BP) and post-pollination (PP). The flowers were hand-dissected into six tissues under the stereomicroscope, including anther (An), filament (Fi), stigma (St), style and ovary (SO), petal (Pe) and sepal (Se). more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21998

57 Samples

Download data: TXT

(Submitter supplied) In order to find the differentially expressed RNAs and signaling pathways related to the dwarf phenotype induced by NlCSP11, 35S-NlCSP11, 35S-XopQ and 35S-GFP control were infiltrated into Nicotiana benthamiana. We analyzed the differentially expressed RNAs in the infiltrated leaves (NlCSP11_Z/XopQ_Z) and the upper uninfiltrated leaves (NlCSP11_U/XopQ_U) of N. benthamiana. KEGG annotation revealed a large number of differentially expressed RNAs involved in plant-pathogen interactions, indicating that NlCSP11 resulted in a more strong systemic resistance in N. more...

Organism:

Nicotiana benthamiana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31115

18 Samples

Download data: TXT

(Submitter supplied) The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here, we developed a novel R-loop profiling technique, ULI-ssDRIP-seq, to decte global R-loops from a limited number of cells. Based on this method, we profiled the R-loop landscapes during parental-to-zygotic transition and early development regulatory in zebrafish, and revealed a series of important characters of R-loops.

Organism:

Arabidopsis thaliana; Danio rerio; Escherichia coli; synthetic construct

Type:

Other; Expression profiling by high throughput sequencing

4 related Platforms

60 Samples

Download data: BW