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) 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) 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) 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) 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) Total blood white blood cells from two FPIES subjects were treated with 2 foods that were safe for those subjects, 3 foods that were triggers for those subjects, relative to LPS and untreated for each subject

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: MTX, TSV

(Submitter supplied) Cohesin loss-of-function mutations are frequently observed in tumors, but the mechanism is unclear. Here, we found that depletion of RAD21, a core subunit of cohesin, leads to massive genome-wide DNA breaks, up to five-fold, and 147 translocation hotspot genes that are co-mutated with cohesin in multiple cancers. Increased DNA damages are independent of RAD21-loss-induced transcription alteration and loop anchor elimination. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

6 Samples

Download data: TAB

(Submitter supplied) Temperate perennial plants have to adapt their growth in order to survive over winter conditions and protect their tissues by entering into dormancy. The dormancy phenomenon is a complex process regulated by many factors, externals (photoperiod and temperature) or internals through the transport towards the buds. In order to better understand the molecular mechanisms involved in the regulation of dormancy, we conducted a transcriptomic analysis of flower buds from the late flowering sweet cherry cultivar 'Fertard' during dormancy, from October 2017 to March 2018.

Organism:

Prunus avium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33329

18 Samples

Download data: TXT

(Submitter supplied) The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. more...

Organism:

Ambystoma mexicanum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32846 GPL27159

16 Samples

Download data: BW

(Submitter supplied) The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. more...

Organism:

Ambystoma mexicanum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL22800 GPL27159

34 Samples

Download data: BW

(Submitter supplied) The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. more...

Organism:

Ambystoma mexicanum

Type:

Other

Platform:

GPL27159

63 Samples

Download data: BW

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is genome wide association mapping for cold tolerance and yield studies in tomato (Solanum spp.) by phenotyping the genotypes under six diffrent temporal arrangments. Also for conducting quantitative reverse transcription polymerase chain reaction (qRT–PCR) assay of cold tolerant genes.

Organism:

Solanum peruvianum; Solanum pimpinellifolium; Solanum chilense; Solanum lycopersicum var. cerasiforme; Solanum lycopersicum; Solanum habrochaites

Type:

Genome variation profiling by high throughput sequencing

6 related Platforms

50 Samples

Download data: VCF

(Submitter supplied) The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

10 Samples

Download data: H5

(Submitter supplied) MicroRNA172 (miR172) plays a role in regulating a diverse range of plant developmental processes. However, its role in regulating anthocyanin biosynthesis is unclear. In this study, we show that transgenic apple plants over-expressing miR172 show a reduction in red colouration and anthocyanin accumulation in multiple tissue types. This reduction was consistent with decreased expression of APETALA2 homolog MdAP2_1a (a miR172 target gene), MdMYB10, and targets of MdMYB10, as demonstrated by both RNA-seq and RT-PCR analyses. more...

Organism:

Malus domestica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29987

6 Samples

Download data: TXT

(Submitter supplied) Plum pox virus (PPV) causes the serious sharka disease in Prunus trees. Peach [P. persica (L.) Batsch] trees are severely affected by PPV and no definitive source of genetic resistance has been identified at this moment. Previous results showed, however, that PPV-resistant ‘Garrigues’ almond [P. dulcis (Mill.) D.A. Webb] was able to transfer its resistance to ‘GF305’ peach through grafting, preventing these trees from PPV infection and reducing symptomatology and viral load in PPV-infected plants. more...

Organism:

Prunus persica; Prunus dulcis

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL30960 GPL30961

7 Samples

Download data: TXT

(Submitter supplied) Following pathogen infection, plants have developed diverse mechanisms of defense that enhance their immune system for more robust induction of defense responses against recurrent environmental stresses. This induced resistance can be heritable to the progeny, rendering them more tolerant to stressful events. Although within-generational induction of tolerance to abiotic stress is a well-documented phenomenon in virus-infected plants, the transgenerational inheritance of tolerance to abiotic stresses in their progenies has not been explored. more...

Organism:

Nicotiana benthamiana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31115

12 Samples

Download data: TXT

(Submitter supplied) The nervous system requires metabolites and oxygen supplied by the neurovascular network, but this necessitates close apposition of neurons and endothelial cells. We find motor neurons attract vessels with long-range VEGF signaling, but endothelial cells in the axonal pathway are an obstacle for establishing connections with muscles. It is unclear how this paradoxical interference from heterotypic neurovascular contacts is averted. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

22 Samples

Download data: TXT

(Submitter supplied) We analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of Prunus persica and Prunus dulcis and in their F1 hybrid using high-throughput sequencing tecnhologies. We can conclude that the merging of the two parental genomes in the P. persica x P. dulcis hybrid does not result in a “genomic shock” with significant changes in the DNA methylation or in the transcription.

Organism:

Prunus dulcis; Prunus persica x Prunus dulcis; Prunus persica

Type:

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

Platforms:

GPL32038 GPL32040 GPL32039

15 Samples

Download data: TXT