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

PRJNA1031650: Oryza sativa ssp. japonica (Kitaake) stressed by cold stress (5°C, 24 h) targeted to leaves (C-L), roots (C-R) or the whole plant (C), and exposed to previous acclimation (15°C, 12 h)

Source: NCBI / GSE246145
Submission Date: Oct 24 2023
Release Date: Jan 01 2024
Update Date: Aug 27 2024

Summary: The experiment tested organ-specific responses of rice (Oryza sativa ssp. japonica) to cold stress with a special focus on phytohormonal regulation. Cold stress (5°C, 24 h) was applies on the whole plants, leaves or roots. The results showed distinct responses when cold stress was applied on leaves, relating to photosynthesis and sugar synthesis as well as specific changes in phytohormones. On the other hand, stress applied to roots was more similar to the stress on the whole plant indicating roots to be more important in cold stress responses. Acclimation by mild temperature (15°C, 12 h) highlighted changes which are connected even with lower temperature exposure or which are characteristic for untreated organs. Recovery (3 d) indicated ability of plants to restore growth which correlated between individual phytohormones and plant growth. The article connect transcriptome, hormonome, proteome and sugar analyses of rice cold-stress responses.

Overall Design: Comparative gene expression profiling analysis of RNA-seq data from roots of Oryza sativa seedlings grown 13 days in hydroponics, treated for 24 h by cold stress (5°C, 24 h) targeted to leaves, roots or the whole plant. Some plants were pre-treated by acclimation (15°C, 12 h). Some samples were collected after 3-day recovery under control conditions. Three independent biological replicates were collected.

GEN Datasets:
GEND000614
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Cell Line:
Development Stage:
Protocol
Growth Protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Sampling was done 2 h after dawn.; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to cold stress (5°C; the medium and the climate chamber was pre-cooled) for 24 h. Sampling was done 2 h after dawn (12-days-old plants); Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to cold stress (5°C; the medium and the climate chamber was pre-cooled) for 24 h. Sampling was done 2 h after dawn (13-days-old plants); Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to cold stress (5°C; the medium and the climate chamber was pre-cooled) for 24 h. Sampling was done 2 h after dawn (14-days-old plants); Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to cold stress (5°C; the medium and the climate chamber was pre-cooled) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to special thermoregulatory vessels (keeping 20°C of new medium) into pre-cooled chamber (5°C of air) for 24 h. Sampling was done 2 h after dawn (14-days-old plants).; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to special thermoregulatory vessels (keeping 20°C of new medium) into pre-cooled chamber (5°C of air) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to special thermoregulatory vessels (keeping 5°C of new medium) into chamber (20°C of air) for 24 h. Sampling was done 2 h after dawn (14-days-old plants).; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to special thermoregulatory vessels (keeping 5°C of new medium) into chamber (20°C of air) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to cold stress (5°C; the medium and the climate chamber was pre-cooled) for 24 h. Sampling was done 2 h after dawn (14-days-old plants).; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to cold stress (5°C; the medium and the climate chamber was pre-cooled) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to special thermoregulatory vessels (keeping 20°C of new medium) into pre-cooled chamber (5°C of air) for 24 h. Sampling was done 2 h after dawn (14-days-old plants).; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to special thermoregulatory vessels (keeping 20°C of new medium) into pre-cooled chamber (5°C of air) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to special thermoregulatory vessels (keeping 5°C of new medium) into chamber (20°C of air) for 24 h. Sampling was done 2 h after dawn (14-days-old plants).; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to special thermoregulatory vessels (keeping 5°C of new medium) into chamber (20°C of air) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. Sampling of 13-days-old plants was done 2 h after dawn.; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. Sampling of 14-days-old plants was done 2 h after dawn.; Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. Sampling of 17-days-old plants was done 2 h after dawn.
Treatment Protocol: null
Extract Protocol: protocol from Spectrum Plant Total RNA Kit (Sigma-Aldrich)
Library Construction Protocol: performed by sequencing service company (Eurofins Genomics)
Sequencing
Molecule Type: Poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina NovaSeq 6000; Illumina NovaSeq 6001; Illumina NovaSeq 6002; Illumina NovaSeq 6003; Illumina NovaSeq 6004; Illumina NovaSeq 6005; Illumina NovaSeq 6006; Illumina NovaSeq 6007; Illumina NovaSeq 6008; Illumina NovaSeq 6009; Illumina NovaSeq 6010; Illumina NovaSeq 6011; Illumina NovaSeq 6012; Illumina NovaSeq 6013; Illumina NovaSeq 6014; Illumina NovaSeq 6015; Illumina NovaSeq 6016; Illumina NovaSeq 6017; Illumina NovaSeq 6018; Illumina NovaSeq 6019; Illumina NovaSeq 6020; Illumina NovaSeq 6021; Illumina NovaSeq 6022; Illumina NovaSeq 6023; Illumina NovaSeq 6024; Illumina NovaSeq 6025; Illumina NovaSeq 6026; Illumina NovaSeq 6027; Illumina NovaSeq 6028; Illumina NovaSeq 6029; Illumina NovaSeq 6030; Illumina NovaSeq 6031; Illumina NovaSeq 6032; Illumina NovaSeq 6033; Illumina NovaSeq 6034; Illumina NovaSeq 6035; Illumina NovaSeq 6036; Illumina NovaSeq 6037; Illumina NovaSeq 6038; Illumina NovaSeq 6039; Illumina NovaSeq 6040; Illumina NovaSeq 6041; Illumina NovaSeq 6042; Illumina NovaSeq 6043; Illumina NovaSeq 6044; Illumina NovaSeq 6045
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
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