Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: RNA-Seq data of tomato fruit

PROVIDER: PRJNA559455 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9937130_1.fastq.gz	Fastqsanger.gz
	SRR9937130_2.fastq.gz	Fastqsanger.gz
	SRR9937140_1.fastq.gz	Fastqsanger.gz
	SRR9937140_2.fastq.gz	Fastqsanger.gz
	SRR9937131_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [ChIP-seq]

Project description:Here we generated ChIP-seq data of a tomato ERF family TF Sl-ERF_F_4 in red fruit stage and green fruit stage to validate the accuracy of DAP-seq data.

2023-06-30 | GSE173208 | GEO

Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [ChIP-Seq]

Project description:Here, we found that the tomato jmjC domain-containing gene SlJMJ6 encodes a histone lysine demethylase that specifically demethylates H3K27 methylation. Overexpression of SlJMJ6 accelerated fruit ripening in tomato, which is associated with the up-regulated expression of a large number of ripening-related genes. Integrated analysis of RNA-seq and ChIP-seq data identified 55 genes that are targeted directly by SlJMJ6 and transcriptionally up-regulated with decreased H3K27m3 in SlJMJ6 overexpressing (SlJMJ6-OE) fruits. A large number of the SlJMJ6-regulated genes are involved in transcription regulation, ethylene biosynthesis, cell wall degradation, pigment biosynthesis, and hormone signaling. Fourteen ripening-related genes including RIN, ACS4, ACO1, PL, TBG4 were confirmed to be directly regulated by SlJMJ6 through removing H3K27me3. Taken together, these results indicated that SlJMJ6 is a ripening prompting H3K27me3 demethylase that activates the expression of the ripening-related genes by modulating H3K27me3, thereby facilitating fruit ripening in tomato. To our knowledge, this is the first report of the involvement of a histone lysine demethylase in the regulation of fruit ripening.

2020-04-13 | GSE142712 | GEO

Project description:RNA-Seq of tomato fruit

| PRJNA579750 | ENA

Project description:RNA-seq of tomato fruit

| PRJNA972975 | ENA

Project description:Tomato fruit peel RNA-Seq

| PRJNA471364 | ENA

Transcriptomes of Wild Type tomato and sllbd40 fruit on different fruit stages

Project description:In order to find the gene which were regulated by SlLBD40, the fruits of WT and SlLBD40-KO-5 line were collected at 25 DDA to do the RNA-Seq. Total RNA was extracted from above tomato fruits by TRIzol reagent and three biological replicates were taken. The clean data were aligned to the tomato reference genome release SL2.50. According to the RNA-Seq data, many development-related genes were down-regulated in SlLBD40-KO-5 fruit. We find the potential SlLBD40-regulated genes.

2024-12-01 | GSE190128 | GEO

Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [RNA-Seq]

2020-04-13 | GSE142713 | 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

Transcription profiling of tomato fruit responses to Botrytis cinerea

Project description:Tomato fruit ripening is associated with a dramatic increase in susceptibility to the fungal pathogen Botrytis cinerea, the causal agent of gray mold. Mature green fruit, prior to ripening, are largely resistant to B. cinerea, whereas red fruit, at the end of ripening, are susceptible to B. cinerea infection. We used microarrays to detail the gene expression changes that are induced by B. cinerea when tomato fruit at unripe and ripe stages are infected. Experiment Overall Design: Tomato fruit at mature green and red ripe stages were wound inoculated with a water suspension of B. cinerea conidia. Twenty four hours post inoculation fruit pericarp and epicarp tissue around and including the inoculation sites was collected and the total RNA extracted. Total RNA was also collected from healthy and mock inoculated fruit.

2009-06-01 | E-GEOD-14637 | biostudies-arrayexpress

MicroRNAs Associated with AGL6 and IAA9 function in tomato fruit set

Project description:Fruit set is triggered after ovule fertilization, as a consequence of the downregulation of ovary growth repressors, such as the tomato transcription factors Auxin/indole-3-acetic acid 9 (IAA9) and Agamous-like 6 (AGL6). We produced small RNA libraries from IAA9- and AGL6-silenced ovaries to identify miRNAs differentially expressed in IAA9- and AGL6-silenced ovaries as compared with unpollinated control ovaries. The identified miRNAs represent a pool of regulatory sRNAs potentially involved in tomato fruit initiation.

2023-02-19 | GSE225319 | 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