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| Status |
Public on Dec 07, 2021 |
| Title |
001176_P3 |
| Sample type |
SRA |
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| Source name |
AP strain - indoxacarb selected
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| Organism |
Blattella germanica |
| Characteristics |
age: 6th generation
tissue: whole body
treatment: indoxacarb selected
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| Treatment protocol |
Treatment of the selected lines consisted of 60-80% selection of 4-5th instar nymphs over 5 generations with indoxacarb in bait matrix
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| Growth protocol |
Insects were reared under standard laboratory conditions on a diet of Harlan-Teklad 7409 rodent chow, unlimited water, 12:12 light:dark, 25 degrees C and ~65% RH.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from three independent biological replicate samples of 10 whole adult male cockroaches from each of F6-selected and control lines. A two-step process was used that included the Promega SV Total RNA Isolation Kit (Madison, WI, USA) followed by the Bioline TRIsure kit (Tuanton, MA, USA). DNase treatment was included as the final step for the first kit only. The use of two kits ensured the RNA samples were free of excess protein. Total RNA yields ranged from 5.8–18.6 µg with A260/280 and 260/230 ratios in the range of 1.8–2.1. Sample quality was further assessed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) which verified above yields and provided acceptable RIN scores of 7.20-7.76.
RNA samples were enhanced for messenger RNA (mRNA) using the Agilent Tru-Seq RNA prep kit before bar-coded sequencing libraries were made. Sequencing was done on the Illumina HiSeq 2000 platform by the Purdue University Genomics Core (West Lafayette, IN, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Whole body mRNA, selected line, rep 3
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| Data processing |
Sequencing reads were filtered using Phred quality scores and other parameters, and de novo transcriptome assembly performed from all six pooled replicate samples (3 selected and 3 control) using Trinity (Grabherr et al 2011).
Paired reads for individual replicate samples were then mapped to the de novo transcriptome using Bowtie2 (Langmead & Salzberg 2012), which provided read counts used for differential expression analyses
Genome_build: German_cockroach_Trinity.fasta
Supplementary_files_format_and_content: transcriptome assembly fasta file and gene expression counts Excel file
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| Submission date |
Nov 16, 2021 |
| Last update date |
Dec 07, 2021 |
| Contact name |
Michael Scharf |
| E-mail(s) |
[email protected]
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| Organization name |
Purdue University
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| Department |
Entomology
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| Street address |
901 W State St
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| City |
West lafayette |
| State/province |
IN |
| ZIP/Postal code |
47906 |
| Country |
USA |
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| Platform ID |
GPL30962 |
| Series (1) |
| GSE188950 |
Transcriptome responses to defined insecticide selection pressures in the German cockroach |
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| Relations |
| BioSample |
SAMN23183262 |
| SRA |
SRX13149009 |
| 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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