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Items: 1 to 20 of 254441

1.

Methylome comparisons between Red-Flesh and White-Flesh Mesocarps in Red-Flesh apple at 84 Days After Full Bloom (DAFB)

(Submitter supplied) To functionally characterise flesh pigmentation pattern, we performed methylation analysis 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:
Methylation profiling by high throughput sequencing
Platform:
GPL29947
6 Samples
Download data: BED
Series
Accession:
GSE269807
ID:
200269807
2.

Zaxinone Synthase Overexpression Modulates Rice Physiology and Metabolism, Enhancing Nutrient Uptake, Growth, and Productivity

(Submitter supplied) The rice Zaxinone Synthase (ZAS) gene encodes a carotenoid cleavage dioxygenase (CCD) that forms the apocarotenoid growth regulator zaxinone in vitro. Here, we generated and characterized constitutive ZAS-overexpressing rice lines, to better understand ZAS role in determining zaxinone content and regulating growth and architecture. ZAS overexpression enhanced endogenous zaxinone level, promoted root growth and increased the number of productive tillers, leading to about 30% higher grain yield per plant. more...
Organism:
Oryza sativa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27660
12 Samples
Download data: TXT
Series
Accession:
GSE269765
ID:
200269765
3.

Comparative transcriptome reprogramming in oak galls containing sexual or asexual generations of parasitoid wasps

(Submitter supplied) Oak galls form when gall wasps lay their eggs into part of the tree; in some galls, this attachment point to the host consists of only a few cells. The gall itself comprises entirely of host tissue; however, the initiation, development, and physical appearance are controlled by the inducer. This raises the intriguing question of the molecular mechanisms underlying gall formation, by which one or a small number of cells are reprogrammed and commit to a novel developmental path. more...
Organism:
Quercus robur
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33794
27 Samples
Download data: TXT
Series
Accession:
GSE244168
ID:
200244168
4.

Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Arabidopsis thaliana
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL34120 GPL17639 GPL26208
40 Samples
Download data: TXT
Series
Accession:
GSE260822
ID:
200260822
5.

Early-responsive molecular signatures associated with halophytic adaptation in Sesuvium portulacastrum (L.)

(Submitter supplied) Sesuvium portulacastrum (L.) is a halophyte, adapted to grow naturally under high-saline environments. Under control conditions, an inverse correlation was seen between Na and K accumulation, suggesting its facultative nature and ability to use Na-K interchangeably. No significant growth reduction was seen in seedlings upto 250 mM NaCl, except for youngest leaf-curling. Significantly higher accumulation of proline (4.3/1.8-folds), glycine betaine (1.4/1.4-folds) and selected amino-acids (1.4-4.2/1.4-2.3-folds) were seen in root/shoot of seedlings within 8 h stress duration. more...
Organism:
Sesuvium portulacastrum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33503
18 Samples
Download data: CSV, FASTA
Series
Accession:
GSE235196
ID:
200235196
6.

Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of N6-methyladenosine

(Submitter supplied) Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15,000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry. We identify tissue-specific and -enriched proteins that are linked to the functional specificity of individual tissues. more...
Organism:
Oryza sativa
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform:
GPL27660
96 Samples
Download data: BW, CSV
Series
Accession:
GSE229334
ID:
200229334
7.

PLETHORA transcription factors promote early embryo development through induction of meristematic potential

(Submitter supplied) Given that PLTs are key transcription factors in meristems, we hypothesized that loss of activity fails to confer meristematic properties or 'stemness' to the first embryonic cells, leading to developmental arrest. We asked to what degree downstream PLT targets in meristems overlap with those in early embryos. We selected direct PLT target genes by overlaying existing PLT ChIP-seq and DAP-seq datasets. more...
Organism:
Arabidopsis thaliana
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL26208
2 Samples
Download data: NARROWPEAK
Series
Accession:
GSE228358
ID:
200228358
8.

The type Ⅲ effector NopL interacts with GmREM1a and GmNFR5 to promote symbiosis in soybean

(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
Series
Accession:
GSE269425
ID:
200269425
9.

Stress-induced nuclear translocation of transcription factor ONAC023 improves drought and heat tolerance through integrated regulation of multiple processes in rice

(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
Series
Accession:
GSE183241
ID:
200183241
10.

A light signaling factor, ELONGATED HYPOCOTYL 5 (HY5) interacts with Histone deacetylase 9 (HDA9) to play a suppressive role in the glucosinolate biosynthesis in Arabidopsis

(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
Series
Accession:
GSE250418
ID:
200250418
11.

Rhytidome- and cork- type barks of holm oak, cork oak and their hybrids highlight processes leading to cork formation

(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 ilex; Quercus suber; Quercus x morisii
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL33234 GPL33233 GPL33232
16 Samples
Download data: XLSX
Series
Accession:
GSE227020
ID:
200227020
12.

Transcriptome analysis revealed the genes involved in cold stress during flowering from Prunus sibirica

(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
Series
Accession:
GSE204685
ID:
200204685
13.

Transcriptomic analysis between Red-Flesh and White-Flesh Mesocarps in Red-Flesh apple at 84 Days After Full Bloom (DAFB)

(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
Series
Accession:
GSE269214
ID:
200269214
14.

Time-course analysis and transcriptomic identification of a groupⅢ ERF CmTINY2 involved in waterlogging tolerance in chrysanthemums

(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
Series
Accession:
GSE269106
ID:
200269106
15.

RNA-seq analysis of Mpwrky10 in Marchantia under nitrate and phosphate starvation, and comparative analysis with Lactuca sativa var. Redfire

(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
Series
Accession:
GSE238167
ID:
200238167
16.

mDRIP-seq is a high-throughput method for quantitative R-loop landscape profiling

(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:
Mus musculus; Oryza sativa; Saccharomyces cerevisiae; Homo sapiens; Escherichia coli; Arabidopsis thaliana
Type:
Other; Expression profiling by high throughput sequencing
6 related Platforms
384 Samples
Download data: BW, TXT
Series
Accession:
GSE219071
ID:
200219071
17.

mDRIP-seq: a high-throughput method for R-loop mapping and quantitative assessment

(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:
Arabidopsis thaliana; Oryza sativa; Homo sapiens; Mus musculus; Saccharomyces cerevisiae; Escherichia coli
Type:
Other
6 related Platforms
356 Samples
Download data: BW
Series
Accession:
GSE219068
ID:
200219068
18.

Quantification of salinity-induced gene expression in young AGB1-deficient roots

(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
Series
Accession:
GSE264404
ID:
200264404
19.

Transcriptomic analysis of EPFL and Cycloheximide treated clv3 epfl1 epfl2 epfl4 epfl6 mutants

(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
Series
Accession:
GSE243494
ID:
200243494
20.

RNA-Seq analysis reveals the growth of Populus in different light qualities

(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
Series
Accession:
GSE269248
ID:
200269248
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