Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJNA753537

PRJNA753537: The Evening Complex integrates photoperiod signals to control flowering in rice

Source: NCBI / GSE181833
Submission Date: Aug 10 2021
Release Date: May 24 2022
Update Date: Aug 23 2022

Summary: This study aim to understand how the long and short day flowering pathways are integrated and the mechanism of photoperiod perception in rice. Trascriptome at different time points under LD and SD conditions reveal that photoperiodism in rice is controlled by the evening complex. Mutants in LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) orthologs abolish flowering. We show that light causes a rapid and sustained degradation of ELF3-1, and this response is dependent on phyB. ChIP-seq of ELF3 and LUX reveal that EC controls both LD and SD flowering pathways by directly binding and suppressing the expression of key floral repressors, including PRR7 orthologs and Ghd7.

Overall Design: Transcriptome in WT, phyb-1 and elf3-1 elf3-2 lines at multiple points in the day under SD or LD conditions.

GEN Datasets:
GEND000515
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Protocol
Growth Protocol: For the measurement of flowering-time, wild-type, lux, elf3-1, elf3-2, and elf3-1 elf3-2 rice seeds were germinated in water-soaked paper at 28 ºC for 3 days. Germinated seedlings were planted in containers with soil (soil:peat:vermiculite in 2:2:1 volume ratio) and placed in controlled conditions at 28 ºC under 12h/12h light/dark photoperiod (ND conditions) at 70 % humidity.
Treatment Protocol: Plants were grown under 14h/10h (LD conditions) and 10h/14h (SD conditions) photoperiod
Extract Protocol: Homogenizing samples to powder using a freeze cold mortar and pestle followed by total RNA using the RNeasy plant kit (Qiagen), followed by DNAse I treatment (Ambion)
Library Construction Protocol: Prepare high-throughput mRNA sequencing libraries using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)
Sequencing
Molecule Type: rRNA- RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: NextSeq 550
Strand-Specific: Specific
Samples
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Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Condition Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate