Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole-genome transcriptome analysis of tomato and Arabidopsis roots in the shade

ABSTRACT: Whole-genome transcriptome analysis of tomato and Arabidopsis roots in the shade

PROVIDER: PRJNA734360 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Whole-genome transcriptome analysis of tomato and Arabidopsis roots in the shade

Project description:RNA-seq analysis of arabidopsis and tomato roots in shaded and unshaded seedlings.

2023-08-08 | GSE175963 | GEO

Expression data from Arabidopsis plants overexpressing CLE2 in roots

Project description:Plant hormones and small secretory peptides often function as environmental stress mediators. Some recent reports indicate that small secretory peptides, such as CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE), also function as mediators of environmental stimuli. CLE2 is induced in roots by light depriviation. Plants without functional CLE2 showed a chlorosis phenotype when grown under shade. Here, we identified specific genes downstream of CLE2 in roots and shoots with transformed Arabidopsis plants.

2020-12-31 | GSE149015 | GEO

Arabidopsis shade avoidance gene expression in adult plants

Project description:The goal of this study is to obtain genome-wide shade-responsive genes in adult plant. We grew plants under long-day condition with high R/FR ratio (simulated "sun" condition) for two weeks. Plants were treated with shade starting at ZT 4 or left in the sun. We prepared two replicates of each sample at 1 hour and 4 hours after sun and shade treatment and five plants were pooled for each replicate. Cotyledons, hypocotyls, and roots were removed from the samples, leaving leaves and apical tissue.

2015-03-18 | GSE66967 | GEO

Effect of bZIP59 on transcriptional regulation during shade avoidance responses in Arabidopsis

2024-08-18 | GSE227154 | GEO

Shade-induced RTFL/DVL peptides negatively regulate the shade response by directly interacting with BSKs in Arabidopsis

Project description:For shade-intolerant species, shade light indicates the close proximity of neighboring plants and triggers the shade avoidance syndrome (SAS), which causes exaggerated growth and reduced crop yield. We report that nonsecreted ROT FOUR LIKE (RTFL)/DEVIL (DVL) peptides negatively regulate the SAS by repressing the activities of BRASSINOSTEROID SIGNALING KINASEs (BSKs) and PHYTOCHROME INTERACTING FACTOR 4 (PIF4) in Arabidopsis. To identify RTFL function during SAS, we performed RNA-seq to search for differentially expressed genes (DEGs) by comparing transcript levels between Col-0 and dvl1-1D, bsk36, or pif47 seedlings during white light and shade conditions.

2023-09-28 | GSE226205 | GEO

phytochrome A-mediated shade avoidance responses

Project description:Arabidopsis is a shade avioding plant. Under simulated shade light with reduced red-to-far red (R:FR) ratio around 0.7, hypocotyls of Arabidopsis seedlings elongate, which is one of the typical shade avoidance responses.We discovered that when the R:FR ratio further decreases to around 0.1 (strong shade), the shade-induced elongation of hypocotyl is abolished and phytochrome A (phyA) mediates this response.In this study, we aim to examine the difference between shade and strong shade treatment and uncover the role of phyA in regulating the shade avoidance responses.

2019-12-21 | GSE55899 | GEO

Small RNA sequencing in tomato roots with and without Rhizophagus irregularis

Project description:Arbuscular mycorrhizal symbiosis is a predominant relationship between plant and arbuscular mycorrhizal fungi. To idendify arbuscular mycorrhiza responsive miRNAs, small RNA libraries were constructed in tomato roots colonized with Rhizophagus irregularis and without Rhizophagus irregularis. We identify miRNAs in tomato roots and provide a new profile of tomato miRNAs. And we found that some miRNAs were responsive to arbuscular mycorrhiza by comparing miRNAs in treatment with that in control.

2016-07-20 | GSE76204 | GEO

De-phosphorylation of bZIP59 by PP2A ensures appropriate shade avoidance response in Arabidopsis

Project description:Shade can trigger the shade avoidance syndrome (SAS) in shade-intolerant species, which cause exaggerated growth and affect crop yield. We report that Arabidopsis transcription factors bZIP59 negatively regulate SAS. To identify direct targets of bZIP59 at the genome-wide level, we performed ChIP-Seq using ProbZIP59::bZIP59-GFP/bzip59 transgenic plants under white light or transferred to shade conditions for 2 hours. Our results indicated shade light dramatically increased the DNA binding ability of bZIP59, and shade-enhanced binding of bZIP59 majorly located around transcriptional start site (TSS) of genes.

2024-08-18 | GSE236101 | GEO

Epigenetic reprogramming orchestrates transcriptional responses in shade avoidance syndrome of Arabidopsis

Project description:For shade-intolerant plants, changes in light quality indicative of competition from neighboring plants trigger shade avoidance syndrome (SAS). PYHTOCHROME-INTERACTING FACTOR 7 is the major transcriptional regulator of SAS in Arabidopsis. However, the epigenetic reprogramming under shade is poorly understood. To identify the histone chaperone ASF1 and HIRA function during SAS, we performed transcriptome deep sequencing (RNA-seq) to search for differentially expressed genes (DEGs) by comparing transcript levels between Col-0 and pif7-1, asf1ab, or hira-1 seedlings during white light and shade conditions. Our data shown that histone chaperone ASF1, through interacting with PIF7 and helping of HIRA, positively regulates shade-induced genes expression.

2023-01-30 | GSE189669 | GEO

The landscape of mRNA translation in tomato roots

Project description:We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of tomato roots. We generated three biological replicates of RNA-seq and Ribo-seq data for tomato roots. We next used the RNA-seq result for de novo transcriptome assembly and Ribo-seq to identify novel translated open reading frames (ORFs). Our data revealed more than three hundreds of novel translated ORFs on previously unannotated transcripts. Most of the newly identified ORFs are small and difficult to detect with in silico methods. We also identified over thirteen hundreds of upstream ORFs on annotated genes. This data could facilitate gene annotation. Besides, this data also demonstrated that uORFs, miRNAs and antisense RNAs are regulating the expression of associated genes. This study uncovered mechanisms of translational regulation and gene annotation in tomato.

2019-07-05 | GSE124962 | 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