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Sample GSM4396354 Query DataSets for GSM4396354
Status Public on Mar 17, 2020
Title IT3_4
Sample type SRA
 
Source name complete organism
Organism Tetranychus urticae
Characteristics population: IT3
tissue: whole body
Sex: female
age: adult
colour morph: red
resistance status: susceptible to abamectin/milbemectin
Treatment protocol ES1, IT2 and UK6 were highly resistant/resistant against abamectin/milbemectin compared to the susceptible populations RO1 or IT3.
Growth protocol Mites were grown on bean (Phaseolus vulgaris) in controlled condition, 25 ± 1°C, 60 % RH and 16:8 h (L:D) photoperiod.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description PolyA RNA
processed data file: read_count_all_final.txt
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.
 
Submission date Mar 06, 2020
Last update date Mar 17, 2020
Contact name Wannes Dermauw
E-mail(s) wannes.dermauw@ugent.be
Phone 003292646192
Organization name University Ghent
Department Crop Protection
Lab Agrozoology
Street address Coupure Links 653
City Ghent
ZIP/Postal code 9000
Country Belgium
 
Platform ID GPL23384
Series (1)
GSE146593 Geographical distribution and molecular insights into abamectin and milbemectin cross-resistance in European field populations of Tetranychus urticae
Relations
BioSample SAMN14323131
SRA SRX7867448

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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