Ontology highlight
ABSTRACT:
PROVIDER: PRJNA587335 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10389684_1.fastq.gz | Fastqsanger.gz | |||
| SRR10389684_2.fastq.gz | Fastqsanger.gz | |||
| SRR10389685_1.fastq.gz | Fastqsanger.gz | |||
| SRR10389685_2.fastq.gz | Fastqsanger.gz | |||
| SRR10389686_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Apple is one of the most popular fruit crops world-wide and its skin color is an important quality consideration essential for commercial value. However, the strategy on genetic breeding for red skin apple and the genetic basis of skin color differentiation is very limited and still largely unknown. Here, we reported a bud sport mutant of Fuji apple with red skin color and enhanced anthocyanins accumulation. Quantitative SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) proteomics investigations revealed proteome changes in the apple red skin bud mutation and a total of 411 differentially expressed proteins were identified in apple skin. The mutant showed significantly increased expression levels of photosynthesis-related proteins, stress-related proteins as well as anthocyanins biosynthesis pathway. On the other hand, substanial downregulation of mitogen-activated protein kinase 4 (MAPK4) and mevalonate kinase (MVK) were detected. We also hypothesize that a post-transcriptional regulation of the skin color formation occurs in the mutant through the advanced SWATH-MS analysis. Overall, our work provide important information on the application of proteomic methods for analysing proteomes changes in Fuji apple and highlights a clade of regulatory proteins potentially contributed to the fruit skin color formation.
2019-06-18 | PXD011132 | Pride
Project description:we performed RNA-seq and pathways analysis on human preadipocytes isolated from abdominal (A) and gluteofemoral (GF) fat of 10 apple-shaped women and 7 pear-shaped women . Out of the 23,511 annotated transcripts, 636 and 752 genes were differentially expressed in apple- compared to pear-shaped cells in A-FAT and GF-FAT respectively. Interestingly, one of the most significantly over-represented pathways from the apple-specific gene list was “Nucleotide Excision Repair pathway”.
2021-08-19 | GSE176603 | GEO
Project description:transition-Transcriptome of floral transition
| PRJNA477336 | ENA
Project description:Our data showed that lipid and glucose metabolic pathways genes were expressed at higher levels in gluteofemoral adipocyte fraction in pears, while genes associated with inflammation were higher in both abdominal and gluteofemoral apple adipocyte fraction. Gluteofemoral adipocyte chromatin from pear-shaped women contained a significantly higher number of differentially open ATAC-seq peaks relative to chromatin from the apple-shaped gluteofemoral adipocytes. In contrast, abdominal adipocyte chromatin openness showed few differences between apple and pear-shaped women. We revealed a correlation between gene transcription and open chromatin at the proximity of the TSS of some of the differentially expressed genes.
2020-06-08 | GSE143449 | GEO
Project description:Our data showed that lipid and glucose metabolic pathways genes were expressed at higher levels in gluteofemoral adipocyte fraction in pears, while genes associated with inflammation were higher in both abdominal and gluteofemoral apple adipocyte fraction. Gluteofemoral adipocyte chromatin from pear-shaped women contained a significantly higher number of differentially open ATAC-seq peaks relative to chromatin from the apple-shaped gluteofemoral adipocytes. In contrast, abdominal adipocyte chromatin openness showed few differences between apple and pear-shaped women. We revealed a correlation between gene transcription and open chromatin at the proximity of the TSS of some of the differentially expressed genes.
2020-06-08 | GSE143448 | GEO
Project description:allomyrina dichotoma spindle shaped cells
| PRJDB4830 | ENA
Project description:We found that the non-essential amino acid L-Proline (L-Pro) acts as a signaling molecule that promotes the conversion of embryonic stem cells (ESCs) into mesenchymal-like, spindle-shaped, highly motile, invasive pluripotent stem cells. This embryonic stem cell-to-mesenchymal-like transition (esMT) is accompanied by a genome-wide remodeling of the transcriptome We used microarrays to elucidate whether a diverse transcriptional program is the basis of the morphological and motility differences between ESCs and L- Proline treated ESCs (PiCs) Total RNA was extracted from Control (ESCs) and L-Proline treated mouse embryonic stem cells (PiCs) and hybridized on Affimetrix microarrays.
2013-09-05 | E-GEOD-50603 | biostudies-arrayexpress
Project description:miRNAs were important regulators involving in plant-pathogen interactions. However, their roles in apple response to Valsa canker pathogen (Valsa mali, Vm) infection were poorly understood. In this study, we constructed two miRNA libraries using the bark tissues of apple twig (Malus domestica Borkh “Fuji”) inoculated with Vm (IVm) and PDA medium (control, BMd). Among the all miRNAs, 23 miRNAs were specifically isolated in BMd and 39 miRNAs were specifically isolated in IVm. Compared with BMd, the expression of 294 miRNAs decreased, and 172 miRNAs increased in IVm, respectively. We also identified the target genes of these miRNAs using degradome sequencing technology. In total, 353 differentially expressed miRNAs during the pathogen infection were detected to target 1 077 unigenes with 2 251 cleavage sites. Based on GO and KEGG analysis, the genes were found to be mainly related to transcription regulation and signal transduction. We further selected 17 miRNAs and 22 corresponding target genes to detect the expression profiles during pathogen infection. The results indicate that most of them are involved in apple twig-Vm interaction. What’s more, miRNAs and their corresponding target genes seem to regulate the apple twig-Vm interaction by forming many complicated regulation networks. It is worth that a conserved miRNAs mdm-miR482b, which was down regulated in IVm compared with BMd, has 14 potential target genes, and most of them were disease resistance related genes. More important, the feedback regulation of sRNA pathway in apple twig was much more complex and critical in the interaction between apple bark tissue and V. mali. The results provide insights into the crucial functions of miRNAs in the woody plant, apple tree-Vm interaction.
2017-10-11 | GSE104752 | GEO