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| Status |
Public on Mar 17, 2020 |
| Title |
UK6_4 |
| Sample type |
SRA |
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| Source name |
complete organism
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| Organism |
Tetranychus urticae |
| Characteristics |
population: UK6
tissue: whole body
Sex: female
age: adult
colour morph: green
resistance status: resistant to abamectin/milbemectin
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| Treatment protocol |
ES1, IT2 and UK6 were highly resistant/resistant against abamectin/milbemectin compared to the susceptible populations RO1 or IT3.
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| Growth protocol |
Mites were grown on bean (Phaseolus vulgaris) in controlled condition, 25 ± 1°C, 60 % RH and 16:8 h (L:D) photoperiod.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 100-120 adult female mites of each T. urticae population using the RNeasy Plus mini kit (Qiagen, Belgium) with four-fold biological replication for each population. The quality and quantity of the total RNA were analyzed by a DeNovix DS-11 spectrophotometer (DeNovix, USA) and by running an aliquot on a 1% agarose gel.
Illumina libraries were constructed with the TruSeq Stranded mRNA Library Preparation Kit with polyA selection (Illumina, USA).
For RO1, IT2, IT3 and ES1, RNAseq libraries were sequenced on an Illumina HiSeq 2500 to generate strand-specific paired reads of 2 x 125 bp (library construction and sequencing were performed at the Genomics Core Facility of the University of Utah, Utah, USA) while for UK6, RNAseq libraries were sequenced on an Illumina HiSeq 3000 to generate strand-specific paired reads of 2 x 150 bp (NXTGNT sequencing platform, Ghent University, Ghent, Belgium).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
PolyA RNA
processed data file: read_count_all_final.txt
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| Data processing |
The quality of the reads was verified using FASTQC version 0.11.5 (HiSeq 2500 sequencing data) and FASTQC 0.11.8 (HiSeq 3000 sequencing data).
All reads were aligned to the T. urticae three pseudochromosome assembly (Wybouw et al. 2019, doi: 10.1534/genetics.118.301803) using STAR version 2.5.x (Dobin et al. 2013, doi: 10.1093/bioinformatics/bts635) with a 2-pass mode and a maximum intron size (--alignIntronMax) of 20 kb, without the use of the GFF annotation file, and with --sjdbOverhang 124 (for HiSeq 2500 sequencing data) or --sjdbOverhang 149 (for HiSeq 3000 sequencing data).
Next, read counts per gene were obtained using the htseq-count script included in the HTSeq package (Anders et al. 2015, doi: 10.1093/bioinformatics/btu638) with the following settings "-f bam -r pos -s reverse -i Parent" and a GFF3 annotation file ((Tetranychus_urticae_2016.transformed.GenomeTools.gff3), see genome build).
Genome_build: T. urticae three pseudochromosome assembly, included in GEO upload (Tetranychus_urticae_2016.transformed.GenomeTools.gff3.txt, Tetranychus_urticae_3Chr.fasta).
Supplementary_files_format_and_content: read_count_all_final.txt: Tab-delimited text file including raw read counts (HTSeq) per T. urticae gene ID for each sample.
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| Submission date |
Mar 06, 2020 |
| Last update date |
Mar 17, 2020 |
| 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 |
GPL28237 |
| Series (1) |
| GSE146593 |
Geographical distribution and molecular insights into abamectin and milbemectin cross-resistance in European field populations of Tetranychus urticae |
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| Relations |
| BioSample |
SAMN14323124 |
| SRA |
SRX7867456 |
| 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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