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Status |
Public on Dec 30, 2020 |
Title |
D-0d-1 |
Sample type |
SRA |
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Source name |
Solanum lycopersicum:drought
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Organism |
Solanum lycopersicum |
Characteristics |
cultivar: M82 tissue: leaves developmental stage: Thirty-eight days old seedings stress: drought-0d
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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.
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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.
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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
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Submission date |
May 27, 2020 |
Last update date |
Dec 30, 2020 |
Contact name |
WANG QI QI |
E-mail(s) |
wangqiqi_nwafu@sina.com
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Organization name |
Northwest A&F University
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Street address |
No.3,TaiCheng Road
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City |
YangLin |
ZIP/Postal code |
712100 |
Country |
China |
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Platform ID |
GPL19694 |
Series (1) |
GSE151277 |
Transcription profiles of tomato (Solanum lycopersicum) seedlings response to drought and heat stress |
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Relations |
BioSample |
SAMN15032852 |
SRA |
SRX8405728 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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