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| Status |
Public on May 15, 2021 |
| Title |
(Z)-3-HP exposed plant3 |
| Sample type |
SRA |
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| Source name |
Apical part of tomato plant
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| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: Apical part of tomato plant
cultivar: Moneymaker
age: four weeks of age
treatment: (Z)-3-HP exposed plant
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| Treatment protocol |
To carry out these exposures cards of 2 x 2 cm filter paper (volatile emitter) were impregnated each with 10 µl of each corresponding volatile at a concentration of 1:10,000 or in the case of the control 1:10,000 methanol:water.Two impregnated cards with the corresponding volatile were placed in the bottom part of a 30 × 30 × 30 cm plastic cage (BugDorm-1 insect tents) together with an intact tomato. Plants and volatiles were kept undisturbed for 24 hours in isolated climatic chambers to avoid any volatile interference and maintained at at 25 ± 2ºC, 65 ± 10% RH and a 14:10 h (L:D) photoperiod.
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| Growth protocol |
Moneymaker seeds were sown in soil. Two weeks after germination seedlings were individually transplanted into pots (8 × 8 × 8 cm). Plants were maintained undisturbed at 25 ± 2 ºC, with constant relative humidity of 65% ± 5% and a photoperiod of 14:10 h (light: dark). Pesticide-free tomato plants were used for the experiments at four weeks of age (approximately 20 cm high).
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| Extracted molecule |
total RNA |
| Extraction protocol |
The apical part of the tomato plant samples were immediately ground in liquid nitrogen. Portions of the ground samples were used for RNA extraction. Total RNA was extracted using a Plant RNA Kit (Omega Bio-Tek Inc., Doraville, GA, USA) and was treated with RNase-free DNase (Promega Corporation, Madison, Wisconsin, USA) to eliminate genomic DNA contamination.
The library was constructe using TruSeq Stranded mRNA LT Sample Prep Kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
tomato_plant7
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| Data processing |
Illumina HiSeq 4000 reads were trimmed and clipped for quality control in Trimmomatic 0.32. Adapter sequences and bases with base quality lower than 3 from the ends were removed. Using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Reads with length shorter than 36bp are dropped to produce trimmed data.
Read quality was checked for each sample using FastQC v0.11.5. Reads over score of 20 (99% accuracy) are accepted as good quality
Reads were mapped using HISAT2 version 2.0.5, Bowtie2 2.2.6
Known genes and transcripts are assembled with StringTie version 1.3.3b based on reference genome model . The abundance of gene/transcript is calculated in the read count and normalized value as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and as TPM (Transcripts Per Kilobase Million) for a sample.
Genome_build: SL2.50_GCF_000188115.3
Supplementary_files_format_and_content: tab-delimited text files include coverage,RPKM and TPM values for each gene in a sample; gtf files include coverage, RPKM and TPM values per gene, transcripts and exons
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| Submission date |
May 15, 2020 |
| Last update date |
May 16, 2021 |
| Contact name |
Alberto Urbaneja |
| E-mail(s) |
aurbaneja@ivia.es
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| Organization name |
Instituto Valenciano de Investigaciones Agrarias
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| Street address |
Carretera CV-315 Km 10,7
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| City |
Moncada |
| State/province |
Valencia |
| ZIP/Postal code |
46113 |
| Country |
Spain |
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| Platform ID |
GPL25655 |
| Series (1) |
| GSE150659 |
Eliciting plant defenses by exposition to HIPV’s: a new sustainable approach to manage agricultural pests |
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| Relations |
| BioSample |
SAMN14933011 |
| SRA |
SRX8348932 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4555881_tomato_plant7.gene_abund.anno.tab.gz |
680.6 Kb |
(ftp)(http) |
TAB |
| GSM4555881_tomato_plant7.gtf.gz |
4.7 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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