GEO DataSets

(Submitter supplied) Soft rot or Rhizopus rot, caused by the fungal pathogen Rhizopus stolonifer, is an aggressive postharvest disease that affects many fruit and vegetables. We proposed that R. stolonifer displays a necrotrophic behavior when infecting fruit, actively killing the host tissues to complete its life cycle. We tested this hypothesis by identifying R. stolonifer infection strategies when interacting with four fruit hosts (tomato, grape, strawberry, and plum). more...

Organism:

Fragaria x ananassa; Prunus domestica; Solanum lycopersicum; Vitis vinifera; Rhizopus stolonifer

Type:

Expression profiling by high throughput sequencing

5 related Platforms

49 Samples

Download data: CSV

(Submitter supplied) Viromes of sour and sweet cherry trees in Hungarian germ line collections were surveyed using small RNA HTS as an unbiased method. RNA from leaf samples of different cultivars were purified and used to produce seven pools from which small RNA HTS libraries were prepared. The sequenced reads were analyzed using bioinformatic methods to revel the presence of viruses in the samples. Presence of the viruses were validated using RT-PCR.

Organism:

Prunus avium; Prunus cerasus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL33434 GPL23007

7 Samples

Download data: TXT

(Submitter supplied) We explored seasonal gene expression profiles in the Yoshino cherry trees (Cerasus × yedoensis ‘Somei-yoshino’) at three distinct sites, each situated at varying latitudes in Japan. Our goal was to gather molecular phenology data that could provide insights into mechanism of bud dormancy. The molecular phenology approach, which monitors the seasonal dynamics of global gene expression profiles in leaves and buds under natural conditions, enables the study of physiological responses to seasonal environmental changes at the molecular level.

Organism:

Prunus yedoensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33868

90 Samples

Download data: TSV

(Submitter supplied) The experiment was designed to assess the effect of PLX4720 on the gene expression in human primary melanoma-associated fibroblast co-cultired with 5555 mouse melanoma cells

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

8 Samples

Download data: TXT

(Submitter supplied) Xylella fastidiosa is a plant pathogenic bacterium that has been introduced in the European Union (EU), threatening the agricultural economy of relevant Mediterranean crops such as almond (Prunus dulcis). Plant defense elicitor peptides would be promising to manage diseases such as almond leaf scorch but their effect on the host has not been fully studied. In this work, the response of almond plants to the defense elicitor peptide flg22-NH2 was studied in-depth using RNA-seq, confirming the activation of the salicylic acid and abscisic acid pathways. more...

Organism:

Prunus dulcis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32033

16 Samples

Download data: TXT

(Submitter supplied) Through transcriptome sequencing analysis of clones with strong freezing resistance (338) and weak freezing resistance (28) of Prunus sibirica，a total of 6001 significantly differentially expressed genes were obtained. Among them, there are 2070 up-regulated genes and 3,931 down-regulated genes. Differential genes are compared and screened, and WRKY, NAC, bHLH, MADS, MYB, Homeobox, F-box, ZEP, SBT, ERF, CAMTA, MDH, etc. more...

Organism:

Prunus sibirica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30412

6 Samples

Download data: XLS

(Submitter supplied) Thinning is indispensable practice in peach cultivation aiming to reduce fruit number per plant, promoting sink-source balance and reducing competition among fruit, which results in bigger fruit and the improvement of other fruit-quality parameters. Inhibition of floral induction by GAs has been largely demonstrated and commercial products based on GAs have been used to this aim. We tested a product GA4/7 based in different moments after full bloom in peach to reduce the number of flowers in the following season. more...

Organism:

Prunus persica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32039

18 Samples

Download data: TXT

(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) Pseudomonas syringae pv. syringae 9644 (Pss9644) is a causal agent of bacterial cherry canker causing necrotic symptoms on leaves, fruits, gummosis and canker in woody tissues of sweet cherry (Prunus avium). To understand which virulent factor genes were expressed in vitro, Pss9644 was grown in rich media (King's B Broth) and minimum media (hrp-inducing minimum media). The latter mimics the in planta environment.

Organism:

Pseudomonas syringae pv. syringae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34164

6 Samples

Download data: TXT

(Submitter supplied) Using next-generation sequencing (NGS) combined with bioinformatics tools, we characterized two major 5’copy-back defective interfering (5’cb DI) genomes generated during SAD replication. Furthermore, we identified a specific interaction of 5’cb DI genomes and RIG-I that correlated with a high stimulation of the type I IFN signaling

Organism:

Homo sapiens; Rabies virus SAD B19; Lyssavirus rabies

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL31905 GPL31906

36 Samples

Download data: CSV

(Submitter supplied) The vast majority of traditional almond varieties are self-incompatible and the level of variability of the species is very high, resulting in a highly heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level. more...

Organism:

Prunus dulcis; Prunus persica

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21993 GPL27530

12 Samples

Download data: FASTA, TXT

(Submitter supplied) Spring frost is a growing risk to temperate fruit production as warmer winter conditions can lead to earlier bloom, increasing the chance of damaging cold temperatures. One strategy to minimize the impacts of frost is to breed late-flowering cultivars to avoid the frost risk period. In this study, we analyzed Late-Flowering Peach (LFP) germplasm and showed its floral buds require longer chilling and warming periods during dormancy than the control cultivar, ‘John Boy’ (JB). more...

Organism:

Prunus persica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25275

84 Samples

Download data: CSV

(Submitter supplied) Trees with weeping shoot architectures are valued for their beauty and are a resource for understanding how plants regulate posture control. The Prunus persica (peach) weeping phenotype, which has elliptical downward arching branches, is caused by a homozygous mutation in the WEEP gene. Until now, little was known about the function of WEEP protein despite its high conservation throughout Plantae. Here, we present the results of anatomical, biochemical, biomechanical, physiological, and molecular experiments that provide insight into WEEP function. more...

Organism:

Prunus persica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28214

32 Samples

Download data: XLSX

(Submitter supplied) Botrytis cinerea (gray mold) is one of the most destructive pathogens of cherry tomatoes, causing fruit decay and economic loss. Fludioxonil is an effective fungicide widely used for crop protec-tion and is essential for controlling tomato gray mold. The emergence of fungicide-resistant strains has made the control of Botrytis cinerea more difficult. While the genome of Botrytis cinerea is available, there are few reports regarding the large-scale functional annotation of the genome using expressed genes derived from transcriptomes, and the mechanism(s) underlying such flu-dioxonil resistance remain unclear. more...

Organism:

Botrytis cinerea

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32786

18 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL19057

25 Samples

Download data: MTX, TSV

(Submitter supplied) Organ injury stimulates the formation of new capillaries to restore blood supply raising questions about the potential contribution of neoangiogenic vessel architecture to the healing process. With single-cell mapping we resolved the properties of endothelial cells that organize a polarized scaffold at the repair site of lesioned peripheral nerves. Transient reactivation of an embryonic guidance program is required to orient neovessels across the wound. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

20 Samples

Download data: TSV

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

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL26208 GPL21785 GPL24270

361 Samples

Download data

(Submitter supplied) In sexually propagating organisms, genetic and epigenetic mutations are evolutionarily relevant only if they occur in the germline and provide inherited information to the next generation. In contrast to most animals, plants are thought to lack an early segregating germline, implying that somatic cells can contribute genetic information to the progeny if they differentiate into meiocytes. Here we demonstrate that two ARGONAUTE proteins, AGO5 and AGO9, are expressed in the reproductive lineage throughout development and mark an early-segregating germline. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24270 GPL26208

67 Samples

Download data: CSV

(Submitter supplied) Plant-based diets could be a key source of microRNAs in animals. Plant microRNAs are cross-kingdom gene expression regulators that could modulate mammalian gene expression, influencing their physiology. Therefore, it is important to identify the microRNA expression profile of plant foods in order to identify potential target genes and biological functions in the mammalian host. Next-generation sequencing was applied to identify microRNAs in RNA samples derived from nuts (walnut and almond), vegetables (spinach) and fruits (orange, apple, olive, pear, and tomato). more...

Organism:

Citrus sinensis; Prunus dulcis; Juglans regia; Spinacia oleracea; Malus domestica; Solanum lycopersicum; Olea europaea; Pyrus communis

Type:

Non-coding RNA profiling by high throughput sequencing

8 related Platforms

8 Samples

Download data: XLSX

(Submitter supplied) Targeted genome editing holds great promise in biology. However, efficient genome modification, including gene knock-in, remains an unattained goal in multiple cell types and loci due to poor transfection efficiencies and low target genes expression, impeding the positive selection of recombined cells. Here, we describe a genome editing approach to achieve efficient gene targeting using hard to transfect erythroid cell lines. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

4 Samples

Download data: BED