Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of transcriptomes for developing fruits derived from sweet orange varieties

ABSTRACT: Transcriptome comparsions and integrated systems analysis were used to identify candidate genes associated with fruit acidity control and gene coexpression subnetworks involved in fruit acid accumulation. mRNA profiles of fruit tissues at two stages (45 days postanthesis (DPA); and 142 DPA) from four varieties with differing fruit acidity.

ORGANISM(S): Citrus sinensis

SUBMITTER: Zhi-Liang Zheng

PROVIDER: E-GEOD-78046 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq analysis of transcriptomes for developing fruits derived from sweet orange varieties

Project description:Transcriptome comparsions and integrated systems analysis were used to identify candidate genes associated with fruit acidity control and gene coexpression subnetworks involved in fruit acid accumulation.

2016-04-13 | GSE78046 | GEO

Genome-wide profiling of microRNAs target transcripts in sweet orange

Project description:miRNAs-mediated gene silencing pathway plays vital roles in plant development, abiotic and biotic stress responses. Here, we carried out a high-throughput sequencing approach to identify miRNAs targets in leaves, flowers and fruit of sweet orange.C onsequently, 55257, 62365 and 19393 degraded mRNA fragments were identified in leaf, flower and fruit, respectively. miRNAs-mediated degraded fragments sequencing of the leaves, flowers and fruit in sweet orange

2014-10-21 | E-GEOD-46764 | biostudies-arrayexpress

Genome-wide profiling of microRNAs in sweet orange

Project description:miRNAs-mediated gene silencing pathway plays vital roles in plant development, abiotic and biotic stress responses. Here, we carried out a high-throughput sequencing approach to identify miRNAs in leaves and flowers of sweet orange. Consequently we identified genome-wide 183 known miRNAs and 38 novel miRNAs. Small RNA sequencing of the leaves and flowers in sweet orange

2014-10-21 | E-GEOD-46747 | biostudies-arrayexpress

Expression data for sweet orange fruits in different development stages

Project description:Citrate is demonstrated to be an indispensable secondary metabolite in citrus fruit. Citrus citrate content is affected by accumulation, degradation, usage, transport and storage. The detail mechanisms of citrate accumulation are complicated in citrus fruit and there are other regulating pathways that have yet to be discovered. In this study, we utilized genomic expression investigation to gain a deep insight into the citrate-accumulation-related biological processes in sweet orange.

2018-04-30 | GSE80190 | GEO

44K Agilent microarray analysis of SlBIM1a overexpressing tomato fruits

Project description:The steroid hormone brassinosteroids (BRs) play considerable roles in plant development and defence. Harnessing the extensive knowledge on Arabidopsis BR signalling network for improving productivity in crop species requires first to identify the conserved network components and their function in the target species. To investigate the function of SlBIM1a, the tomato closest homolog of AtBIM1, which is highly expressed in the developing fruit, we generated transgenic tomatoes, which overexpress or down-regulate SlBIM1a gene. Main alterations were observed in SlBIM1a overexpressing lines, which displayed a severe plant and fruit dwarfism. To unravel the molecular basis of phenotypical modifications in SlBIM1a overexpressing fruits, a microarray (Agilent) analysis was performed on Pro35S:SlBIM1aOX and WT fruits harvested at 15 DPA.

2020-10-26 | E-MTAB-9502 | biostudies-arrayexpress

Transcriptomic difference between the wild type red-fruited tomato and its yellow-fruited mutant

Project description:Background: Fruit color is an important quality trait for nutrition value in tomato (Solanum lycopersicum) and has attracted huge attention for a long time. In order to dissect the yellow-fruit color of a novel tomato mutant n3122, we compared the dynamic transcriptome of the fruit pericarps from the mutant n3122 and its wild type red-fruited tomato cultivar M82. Results: The transcriptomes of fruits from M82 35 DPA (Days Post Anthesis), M82 47 DPA, M82 54 DPA, n3122 35 DPA, n3122 47 DPA, n3122 54 DPA and n3122 60 DPA were sequenced using an Illumina Hiseq 2000 sequencing platform. A total of 5568 differentially expressed genes (DEGs) were commonly identified in the four pairwise comparisons of M82_35 DPA vs n3122_35 DPA, M82_47 DPA vs n3122_47 DPA, M82_54 DPA vs n3122_54 DPA and M82_47 DPA vs n3122_60 DPA. Further Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that carotenoids biosynthesis, ethylene biosynthesis and signaling transduction, and transcription factors associated fruit ripening were different between M82 and n3122 which might be the underlying mechanisms for the yellow-fruit color of tomato. Conclusions: This research provided a global data set of dynamic transcriptomic changes during fruit development and ripening for the wild type red-fruited tomato cultivar M82 and its yellow-fruited mutant n3122, and offered a base for elucidating the molecular mechanisms underlying tomato red/yellow fruit color mutation.

2017-04-10 | GSE73908 | GEO

RNA sequencing Reveals the Differentially Expressed Genes between Wild-type and SlDof1-RNAi Fruits

Project description:Purpose: To identify genes regulated by SlDOF1 during fruit ripening, we performed RNAseq experiments with three biological replicates and compared the transcriptom profiles of SlDOF1-RNAi and wild-type fruit at breaker stage. Methods: Expression profiles of wild-type (wt) and SlDof1-RNAi fruits (SlDof-8-RNAi) at 38 days after poliation (dpa) were generated by deep sequencing with three replicates using Illumina HiSeqTM 2000. RNA-seq reads obtained from the replicate were further filtered and aligned against the whole tomato genome. Differential expressed genes between samples were defined by DESeq software using two separate models, based on PPEE > 0.05 and false discovery rate (FDR)<0.001. Quantitative RT–PCR was performed using SYBR Green assays. Results: A total of 1728 differentially expressed genes were identified in the SlDof1 RNAi fruit compared with the wild type and among them were a number of ripening-relate genes.

2020-12-01 | GSE119493 | GEO

RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 that is required for tomato fruit ripening

Project description:For exploring whether mRNA m6A modification participates in the regulation of tomato fruit ripening, we performed m6A-seq in three tomato fruit samples, including wild-type (WT) at 39 days post-anthesis (DPA) and 42 DPA, and Cnr mutant at 42 DPA, with three biological replicates. mRNA methylome analysis reveals that m6A methylation is a prevalent modification in mRNA of tomato fruit and the m6A sites are predominantly enriched in the stop codon and 3’ untranslated region, where m6A deposition has been proved to negatively correlate with gene expression. Hundreds of ripening-induced and ripening-repressed genes, including the SlDML2, were found to harbour changed m6A levels during fruit ripening or in the Cnr mutant, implicating the involvement of m6A modification in the regulation of fruit ripening.

2019-07-19 | GSE125306 | GEO

N6-methyladenosine RNA methylomes in woodland strawberry fruit at three different development stages.

Project description:For exploring whether mRNA m6A modification participates in the regulation of strawberry fruit ripening, we performed m6A-seq in woodland strawberry fruit at three different development stages, including the S6 stage (almost 15 days post-anthsis (DPA)), the RS1 stage (21 DPA), and the RS3 stage (27 DPA), with three biological replicates. mRNA methylome analysis reveals that m6A methylation prevalently distributes in the strawberry transcriptome and highly enrichs in the coding sequence, stop codon and 3’ untranslated region.

2021-05-17 | GSE167183 | GEO

Transcriptome analysis of Eggplant (Solanum melongena L.) cv. PPL during fruit development and ripening.

Project description:Transcriptome analysis of Eggplant cv. PPL during fruit development at 0, 5, 10, 20 and 50 dpa. Eggplant is third most important solanaceae crop species after potato and tomato. It is a versatile crop adapted to different agro-climatic regions and can be grown throughout the year. Unripe eggplant fruit is consumed as cooked vegetable in various ways. It is low in calories and fats, contains mostly water, some protein, fibre and carbohydrates. To decipher molecular mechanisms involved in fruit development eggplant fruit were collected at 0, 5, 10, 20 and 50 dpa and gene expression profiles were analyzed using Affymetrix tomato GeneChip Genome array.

2014-02-14 | GSE44182 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data