Gene Expression Nebulas
基于标准化流程分析的转录图谱综合数据库

Gene Expression Nebulas

多物种转录图谱整合数据库

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)

来源: NCBI / GSE246145
提交时间: Oct 24 2023
释放时间: Jan 01 2024
最后更新时间: Aug 27 2024

概要: 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.

项目整体设计: 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 数据集:
GEND000614
测序方法:
物种:
组织:
健康状况:
细胞类型:
细胞系:
发育阶段:
方案
生长方案: 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.
处理方案: null
提取方案: protocol from Spectrum Plant Total RNA Kit (Sigma-Aldrich)
建库方案: performed by sequencing service company (Eurofins Genomics)
测序信息
分子类型: Poly(A)+ RNA
库的片段类型: PAIRED
库的链类型: Forward
测序平台: ILLUMINA
测序仪型号: 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
链特异性: Specific
样本
基本信息:
样本描述:
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测序信息:
质量评估:
数据来源 GEN样本编号 GEN数据集编号 系列编号 项目编号 样本编号 样本名称 生物样本编号 样本访问号 实验访问号 释放时间 提交时间 最后更新时间 物种 种族 族裔 年龄 年龄单位 性别 来源名称 组织 细胞类型 细胞亚型 细胞系 疾病 疾病状态 发育阶段 突变/变异 表型 Condition Detail 生长方案 处理方案 提取方案 建库方案 分子类型 库的片段类型 链特异性 库的链类型 加标(Spike-In) 测序方法 测序平台 测序仪型号 细胞数 测序片段数 碱基数 平均测序片段长度_1 平均测序片段长度_2 唯一比对率 多重比对率 覆盖度