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Sample GSM4570190

Query DataSets for GSM4570190

Status

Public on Dec 30, 2020

Title

Heat-0h-3

Sample type

SRA

Source name

Solanum lycopersicum:heat stress

Organism

Solanum lycopersicum

Characteristics

cultivar: M82
tissue: leaves
developmental stage: Thirty-eight days old seedings
stress: Heat-0h

Treatment protocol

Thirty-eight days after sowing (DAS), plants of the same stage with maximum water holding capacity of soil were subjected to 42°C heat stress conditions with 90% relative humidity for 0h (Heat-0h), 2h (Heat-2h), 4h (Heat-4h), 12h (Heat-12h), 24h (Heat-24h) and put back into the optimal conditions mentioned above for 1 d after Heat-24h (Heat-Recovery).When the quality of each nutrient pot is reduced by about 1/5 (i.e. the soil water capacity is about 80%), then it will be counted as the drought treatment control 0d. After this time point, tomato plants of 0d (D-0d), 1d (D-1d), 2d (D-2d), 3d (D-3d), 4d (D-4d), 5d (D-5d) and re-watered and grew in the optimal conditions mentioned above for another 1d (D-Recovery) were respectively selected for drought treatment.

Growth protocol

Seeds of the tomato (S. lycopersicum cv. M82) were obtained from the Tomato Genetic Resource Center, University of California, Davis, CA, USA. Seeds were evenly sown per pot (7 x 7cm pots) with stroma (Nutritive soil :Vermiculite: Perlite=3:1:1) in artificial climate chambers. The climate conditions included: 16/8 h day/night photoperiod, 25°C air temperature, 800 μmol/m2/s1 light intensity, and 70% humidity. Plants were watered daily to meet the optimal water requirement before stress treatment.

Extracted molecule

total RNA

Extraction protocol

Total RNA of these samples were extracted using the TRIzol reagent, according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

The raw paired end reads were trimmed and quality controlled by Trimmomatic with default parameters
Clean reads were separately aligned to reference genome with orientation mode using TopHat software
To identify DEGs (differential expression genes) between two different samples, the expression level for each transcript was calculated using the fragments per kilobase of exon per million mapped reads (FPKM) method.Cuffdiff was used for differential expression analysis.
Genome_build: Current Tomato Genome version SL4.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

Submission date

May 27, 2020

Last update date

Dec 30, 2020

Contact name

WANG QI QI

E-mail(s)

wangqiqi_nwafu@sina.com

Organization name

Northwest A&F University

Street address

No.3，TaiCheng Road