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Sample GSM6043868 Query DataSets for GSM6043868
Status Public on Apr 18, 2022
Title Control_24h_rep1
Sample type SRA
 
Source name leaf
Organism Solanum lycopersicum
Characteristics tissue: leaf
genotype: cv. Better Bush
treatment: Control_24h
Treatment protocol Six tomato plants were infested with 6 larvae deposited on the three terminal leaflets of the 3rd true leaf and six control plants were subject to mock deposition. Two harvests were conducted after 5 h and 24 h of herbivory. At both harvest time, the infested leaflets from which the larvae have been removed (and the corresponding leaflets of the control plant) were sampled, immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Twelve sequencing libraries were created corresponding to 4 conditions in triplicates (Tuta infested 5h and 24h; control 5h and 24h)
Growth protocol Tomato plants (cv. Better Bush) were grown on a Nutrient Film Technique system set in a growth chamber (16h photoperiod, 23°C/18°C day/night in air and 23°C in nutrient solutions, 60% air humidity)
Extracted molecule total RNA
Extraction protocol RNA was harvested using EZNA Plant RNA kit mini plus kit (Omega bio-tek, Norcross, GA, USA). Three micrograms of total RNA were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina HiSeq 2500
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Reads were processed and filtered using the Trimmomatic software
they were mapped on the tomato genome (ITAG2.4) using the BWA-MEM software
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using FeatureCounts software
Assembly: tomato genome (ITAG2.4)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
 
Submission date Apr 14, 2022
Last update date Apr 19, 2022
Contact name Romain Larbat
E-mail(s) romain.larbat@univ-lorraine.fr
Organization name LAE
Department INRAE
Street address 2 avenue de la forêt de Haye
City Vandoeuvre les nancy
ZIP/Postal code 54500
Country France
 
Platform ID GPL19694
Series (1)
GSE200795 Transcriptomic analysis of the tomato plant response to Tuta absoluta herbivory
Relations
BioSample SAMN27584798
SRA SRX14852907

Supplementary file Size Download File type/resource
GSM6043868_Control_24h_rep1.txt.gz 153.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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