GEO DataSets

(Submitter supplied) The establishment of symbiotic interactions between leguminous plants and rhizobia requires complex cellular programming activated by Rhizobium Nod factors (NFs) as well as type III effector (T3E)-mediated symbiotic signaling. However, the mechanisms by which different signals jointly affect symbiosis are still unclear. Here we describe the mechanisms mediating the cross talk between the Sinorhizobium fredii T3E Nodulation Outer Protein L (NopL) effector and NF signaling in soybean. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28801

12 Samples

Download data: CSV

(Submitter supplied) Drought and heat are major abiotic stresses frequently coinciding to threaten rice production. Although hundreds of stress-related genes have been identified in the past two decades, very few genes have been confirmed to confer resistance to multiple stresses in crops. Here we report ONAC023, identified through NAC-centered gene regulatory network and genetic association analyses, is a hub stress-regulator that integrates the regulations of both drought and heat tolerance in rice. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL23876

49 Samples

Download data: BW, TXT

(Submitter supplied) In this study, we found that a light signaling factor, Long Hypocotyl 5 (HY5) is closely involved in the regulation of GSLs contents in light condition. In addition, HY5 was shown to physically interact with a histone deacetylase HDA9 and bind to proximal promoter region of MYB29 and IMD1 to suppress aliphatic GSL biosynthetic process. These results demonstrate that HY5 acts to suppress GSL accumulation at daytime, thus properly modulating the GSL contents on a daily basis of Arabidopsis plant.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: BW

(Submitter supplied) The periderm is basic for land plants due to its protective role during radial growth, which is achieved by the polymers deposited in the cell walls. Despite the research on the topic has unravelled the role of several enzymes and transcription factors, many questions remain open, especially those regarding cell development. Here we use the outer bark of cork oak (cork), holm oak (rhytidome), and their natural hybrids’ to further understand the mechanisms underlying periderm development. more...

Organism:

Quercus suber; Quercus x morisii; Quercus ilex

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33234 GPL33232 GPL33233

16 Samples

Download data: XLSX

(Submitter supplied) Through transcriptome sequencing analysis of clones with strong freezing resistance (CR_453) and weak freezing resistance (NC_371) of Prunus sibirica，a total of 15,228significantly differentially expressed genes were obtained. Among them, there are 6,630 up-regulated genes and 8,598 down-regulated genes. Differential genes are compared and screened, and B3, MYB, AAA, zf-GRF, bHLH, TCP, WD40, HSP, PPR, Zim, AP2, CBF, etc, Freeze-related gene family.It is also found that a large number of gene families are regulated by hormones, including GST_N、Auxin_inducible， Abhydrolase_1，P450，AP2，ADH_N，Zim，HATPase_c，2OG-FeII_Oxy，IPPT，C2，RRM_1and so on.

Organism:

Prunus sibirica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30412

30 Samples

Download data: TXT

(Submitter supplied) To functionally characterise flesh pigmentation pattern, we performed transcriptomic comparisons between RF and WF mesocarps. The transition step between fully red fruits and heterogeneously pigmented fruit were targeted during fruit development (84 Days After Full Bloom - DAFB).

Organism:

Malus domestica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34567

6 Samples

Download data: SF

(Submitter supplied) ‘Hangju’ is a variety of Chrysanthemum morifolium Ramat with both aesthetic and medicinal value, cultivated as traditional Chinese medicine for four centuries. The cultivation of ‘Hangju’ faces a significant challenge due to waterlogging stress, resulting in a considerable decrease in crop yield. Nevertheless, there is a scarcity of studies exploring the underlying mechanisms of waterlogging tolerance in ‘Hangju’. more...

Organism:

Chrysanthemum x morifolium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34560

40 Samples

Download data: TXT

(Submitter supplied) To understand the role of WRKY10 transcription factor in foliar pigmentation patterns in Marchantia (liverwort) and assess the conservation of its regulatory network in Lactuca sativa var. Redfire(angiosperm).

Organism:

Marchantia polymorpha; Lactuca sativa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29850 GPL28764

27 Samples

Download data: CSV

(Submitter supplied) Current methods for R-loop profiling need to perform experiments for each sample individually, with consequent limitations in throughput. Here, based on the barcoding strategy, we develop mDRIP-seq, a high-throughput method showing equivalent performance as conventional methods, but with merits of 7-fold less cost and 6-fold less hand-on time per sample. We also show the simplicity and effectiveness of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. more...

Organism:

Escherichia coli; Arabidopsis thaliana; Mus musculus; Oryza sativa; Saccharomyces cerevisiae; Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

6 related Platforms

384 Samples

Download data: BW, TXT

(Submitter supplied) Current methods for R-loop mapping need to perform DNA:RNA immunoprecipitation for each sample individually, with consequent limitations in throughput. Here, we develop and validate mDRIP-seq, a multi-sample barcoding and pooling method for R-loop mapping. We show mDRIP-seq performs equivalently as conventional methods, but with the merits of high throughput and cost-efficiency. We also show the simplicity of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. more...

Organism:

Saccharomyces cerevisiae; Escherichia coli; Arabidopsis thaliana; Oryza sativa; Homo sapiens; Mus musculus

Type:

Other

6 related Platforms

356 Samples

Download data: BW

(Submitter supplied) To further investigate the gene expression profiles in agb1 mutant seedlings responding to salt stress, we employed whole transcriptome microarray expression profiling as a discovery platform to identify genes with the potential to be regulated by AGB1-mediated signaling cascades. Arabidopsis thaliana 7-day-old wild-type and agb1-3 mutant roots were challenged by immersing in 150 mM NaCl containing MS liquid media for 0 or 4 hours, and 4,830 genes induced by high salinity were identified that distinguished between zero and four hours among wild-type and agb1-3 samples. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL12621

12 Samples

Download data: TXT, XLSX

(Submitter supplied) Maintenance and regulation of the shoot apical meristem size and boundaries are essential for plant growth and leaf organogenesis. Canonically, CLAVATA 1, CLAVATA 3 and WUSCHEL control shoot apical meristem (SAM) size and SAM maintenance. Recently it has been shown that ERECTA (ER) family genes also control SAM size at its boundaries. The ERECTA family of receptor like protein kinases are bound by EPIDERMAL PATTERNING FACTOR LIKE (EPFL) protein ligands. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

12 Samples

Download data: TXT

(Submitter supplied) Light plays a key role in plant growth, development and response to adversity. Plants perceive different wavelengths of light in the environment through various photoreceptors and regulate plant growth and development through light signaling. However, there are fewer studies on the effects of different light qualities on the growth and development of tree species at high altitude. In the study, the effects of blue and green light treatments on the growth and development of Populus cuttings were investigated. more...

Organism:

Populus qamdoensis; Populus schneideri

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34572 GPL34573

18 Samples

Download data: TXT

(Submitter supplied) Histone H2A monoubiquitination (H2Aub1) is a ubiquitous and conserved post-translational modification, playing a non-degradative role in multiple progresses including transcription regulation. In Arabidopsis thaliana, H2Aub1 is mediated by AtRING1s and AtBMI1s, catalytic subunits of Polycomb repressive complex 1 (PRC1). Despite PRC2-associated repressive role of H2Aub1, the mechanism regarding how H2Aub1 distributed on non-H3K27me3 region need to be explained. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

3 Samples

Download data: TXT

(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

(Submitter supplied) The parent-of-origin effect on seed size can result from imprinting or a combinational effect between cytoplasmic and nuclear genomes, but their relative contributions remain unknown. To discern these confounding effects, we generated cytoplasmic-nuclear substitution (CNS) lines using recurrent backcrossing in theArabidopsis thalianaecotypes Col-0 and C24. These CNS lines differ only in the nuclear genome (imprinting) or in the cytoplasm. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19580 GPL17639 GPL26208

32 Samples

Download data: TSV

(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) The root system plays an essential role in plant growth and adaptation to the surrounding environment. Lateral roots (LR) originate postembryonically from a group of pericycle founder cells (FC) that are specified by a root clock in an auxin dependent manner and extend the root´s surface. Auxin perception entails the physical interaction of TIR1 or AFBs proteins with Aux/IAA repressors to form a co-receptor system. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24025

12 Samples

Download data: TXT

(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