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| Status |
Public on Mar 20, 2019 |
| Title |
TOL2: 14196X2_170505_D00294_0319_BCAJ3JANXX |
| Sample type |
SRA |
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| Source name |
complete organism
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| Organism |
Anopheles arabiensis |
| Characteristics |
Stage: 3-5 day old female adult, non-blood-fed
strain/population: Tolay
tissue: complete organism
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| Treatment protocol |
The ASN, CHW and TOL populations were previously shown to be resistant against deltamethrin and DDT (Alemayehu et al., 2017, DOI: 10.1186/s13071-017-2342-y).
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| Growth protocol |
Anopheles arabiensis larvae were collected in the South-West part of Ethiopia from a range of breeding sites: Asendabo (ASN), Chewaka (CHW) and Tolay (TOL). Larvae were reared to adults on site in rooms with standard conditions of 25 ±2oC and a relative humidity of 80 ± 10% for all three respective sites. Larvae were fed with dog biscuits and brewery yeast whereas adults were provided a 10% sucrose solution soaked into cotton pads (Gerberg et al., 1994, ISBN: 0960621083). Two laboratory strains served as a pesticide susceptible population: an Ethiopian strain (Sekoru (SEK)), previously described in Alemayehu et al. (2017, DOI: 10.1186/s13071-017-2342-y), and a strain from Mozambique (MOZ) previously described in Witzig et al. (2013, DOI: 10.1038/hdy.2012.112). Both laboratory strains were reared in a similar way as the three Ethiopian populations collected from the field.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
3-5 days old non-blood-fed An. arabiensis female adult mosquitoes from each population (ASN, CHW or TOL) or strain (SEK, MOZ) were preserved in RNAlater (Ambion, Thermo Fischer Scientific) in a 1.5ml Eppendorf tube. All tubes were stored at -80 oC. Total RNA was extracted from batches of ten female mosquitoes using RNAqueous®-4PCR Kit (Ambion, Thermo Fischer Scientific) protocol. RNA was treated with DNase1 treatment and DNase inactivation according to the instructions of the RNAqueous®-4PCR Kit. Four biological replicates were included for each population and each laboratory strain.
Illumina libraries were constructed with the TruSeq Stranded mRNA Library Preparation Kit with polyA selection (Illumina, USA)
RNAseq, libraries were sequenced on an Illumina HiSeq 2500 to generate strand-specific paired reads of 2 x 125 bp (High-Throughput Genomics Core of the Huntsman Cancer Institute, University of Utah, Utah, USA). Sequenced reads were trimmed by the sequencing facility.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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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 nuclear genome (Neafsey et al., 2015; DOI: 10.1126/science.1258522) and mitochondrial genome (GenBank accession: NC_028212) of An. arabiensis using HISAT2 (Kim et al., 2015; DOI: 10.1038/nmeth.3317) and the following options “--max-intronlen 75000 --rna-strandness RF --known-splicesite-infile splicesites.txt”. The “splicesites.txt” file was generated from the gene transfer format (GTF) files of the nuclear and mitochondrial genome of An. arabiensis using a script accompanying the HISAT2 software (hisat2_extract_splice_sites.py). The AaraD1.6 GTF file (13830 genes of which 13452 are protein coding genes, released 25 April 2017 at VectorBase, (https://www.vectorbase.org/organisms/anopheles-arabiensis/dongola/aarad16) was used for the nuclear genome, while the GTF file for the mitochondrial genome was generated from the GenBank file () using the bp_genbank2gff3.pl and gffread script included in the BioPerl (http://bioperl.org/) and Cufflinks package (Trapnell et al., 2012; DOI: 10.1038/nprot.2012.016), respectively. Resulting BAM files were subsequently sorted by read name using SAMtools version 1.5 (Li et al., 2009; DOI: 10.1093/bioinformatics/btp352).
Next, read counts per gene were obtained using the htseq-count script included in the HTSeq package, version 0.9.0 (Anders et al., 2015; DOI: 10.1093/bioinformatics/btu638), with the following settings “-i gene_id -t exon -f bam -s reverse” and the general feature format 3 (GFF3) version of the previously mentioned An. arabiensis GTF files.
Genome_build: AaraD1 (nuclear genome, release April 30, 2013, see https://www.vectorbase.org/organisms/anopheles-arabiensis/dongola/aarad1) and NC_028212.1 (mitochondrial genome, release November 17, 2015, see https://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/nuccore/NC_028212.1/)
Supplementary_files_format_and_content: Tab-delimited text file includes read counts (HTSeq) for each sample
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| Submission date |
Oct 09, 2018 |
| Last update date |
Mar 20, 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 |
GPL25651 |
| Series (1) |
| GSE121006 |
Genome-wide gene expression profiling of three Ethiopian insecticide resistant Anopheles arabiensis populations and two insecticide susceptible Anopheles arabiensis strains |
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| Relations |
| BioSample |
SAMN10222118 |
| SRA |
SRX4818055 |
| 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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