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| Status |
Public on Oct 02, 2017 |
| Title |
DEM1 |
| Sample type |
SRA |
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| Source name |
complete organism
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| Organism |
Tetranychus urticae |
| Characteristics |
Stage: female adult
strain: JP-R
synergists: DEM
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| Treatment protocol |
Synergists were dissolved in a mixture of N,N-dimethylformamide and emulsifier W (alkylarylpolyglycolether, 3:1 w/w, respectively) and subsequently diluted with deionized water 100-fold. Used concentrations; PBO (1000 ppm), DEF (500 ppm), DEM (2000 ppm) and CsA (50 ppm). Leaf discs were sprayed at 1 bar pressure in a Cornelis spray tower with 650µl spray fluid (1.56 ± 0.04mg fluid deposit cm-2) containing one of the synergists (DEF, DEM, PBO, CsA) or formulation (FORM; N,N-dimethylformamide and emulsifier W (3:1 w/w) diluted in deionized water 100-fold) only. Unsprayed mites (CON) served as an additional control. Next, leaf disks were placed in a climatically controlled room at 26°C, 60% RH with a 16:8h light:dark photoperiod. After 24 hours, living mites were scored and collected for RNA extraction.
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| Growth protocol |
The T.urticae JP-R strain was maintained on potted bean plants, Phaseolus vulgaris L. var. Prelude, sprayed with 200 mg a.i. cyenopyrafen L-1 (STARMITE, 30% SC) until run-off. For the week prior to collection of RNA, the strain was maintained on bean plants without cyenopyrafen selection pressure. About 30 3-5 day old adult females were transferred to the upper (adaxial) side of a 9 cm2 square-cut kidney bean leaf discs placed on wet cotton wool. About 600 mites (20 leaf disks with mites) were used for each treatment (DEF, DEM, PBO or CsA) and for the controls (FORM, CON). After spraying, leaf disks were placed in a climatically controlled room at 26°C, 60% RH with a 16:8h light:dark photoperiod.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from about 100 adult female mites using the RNeasy mini kit (Qiagen, Belgium) with four-fold biological replication for each treatment (PBO, DEF, DEM, CsA) and the controls (FORM, CON).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
counts_combined.txt
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| Data processing |
The quality of the reads was verified using FASTQC version 0.11.4
All reads were aligned to the T. urticae genome using the two-pass alignment mode of STAR 2.5.0a with a maximum intron size set to 20 kb. Resulting BAM files were subsequently sorted on read name by using SAMtools 0.1.19.
Read counts per gene using the most recent T. urticae annotation (version of June 23, 2016) were then obtained using the default settings of HTSeq 0.6.0 with the “STRANDED” flag set to “yes” and the “feature” flag set to “exon”
Genome_build: Grbić, M. et al. The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479, 487–92 (2011).
Supplementary_files_format_and_content: Tab-delimited text file includes read counts (HTSeq) for each sample. Gene IDs are found at http://bioinformatics.psb.ugent.be/orcae/overview/Tetur
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| Submission date |
Apr 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Wannes Dermauw |
| E-mail(s) |
wannes.dermauw@ugent.be
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| Phone |
003292646192
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| Organization name |
University Ghent
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| Department |
Crop Protection
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| Lab |
Agrozoology
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| Street address |
Coupure Links 653
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| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platform ID |
GPL23384 |
| Series (1) |
| GSE98293 |
The effect of insecticide synergist treatment on genome-wide gene expression in a polyphagous pest |
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| Relations |
| BioSample |
SAMN06843509 |
| SRA |
SRX2767747 |
| 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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