 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 03, 2024 |
| Title |
Gypsy Moth Strain CT, Day 5, Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Gypsy Moth Strain CT_Day 5
|
| Organism |
Lymantria dispar dispar |
| Characteristics |
strain: CT
Sex: female
sampling timepoint (day): 5
|
| Treatment protocol |
Larvae were reared in cohorts of 6 at 25±1°C and 60% RH with L:D of 16:8, using methods previously described (Keena 1996). The high wheat germ artificial diet (Bell et al. 1091) was optimized for the individual populations using Wesson salt mix without iron and by adding 0.21 g (RM population) or 0.13 g (CT population) amorphous FePO4/L of diet. Pupae were harvested daily and separated according to sex.
|
| Growth protocol |
Eggs from laboratory colonies were held at 5±1°C and ~100% RH with L:D of 16:8 for 144 days to ensure that diapause requirements were met. All eggs produced by 100 individual females from each geographic population (CT 32nd lab generation and RM 34th lab generation) were mixed together, as is the normal process for maintaining these colonies. From the pool of mixed eggs, packets of about 500 eggs were made. Eggs were incubated at 25±1°C and 60% RH with L:D of 16:8 to initiate hatch.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were homogenized individually in Trizol reagent (Ambion, Life Technologies; 4 to 7 mL depending on the size of the pupa) using 15 mL disposable tissue grinders (VWR, Cat.47732-446). For each sample, 500 µL of the homogenate was transferred to a 1.5 mL microfuge tube, to which another 500 µL of Trizol was added. The tubes were then centrifuged for 4 min at 17,000 x g to pellet debris. 400 µL of the supernatant was subsequently used for RNA extraction using the Direct-zol RNA miniprep kit (Zymo Research). RNAs were eluted using 50 µL of water, quantified using a NanoDrop ND1000 spectrophotometer (Thermo Fisher Scientific Inc.) and assessed for quality using a 2100 Bioanalyzer system (Agilent).
RNASeq libraries and Ion Proton sequencing were performed at the Genomic Analysis Platform of the Institute of Integrative and Systems Biology (Laval University, Quebec, QC, Canada) using the NEBNext Ultra II directional RNA library prep kit (New England BioLabs) with the NEBNext Poly (A) mRNA magnetic isolation module. Ion Proton sequencing was performed on an Ion Chef with a P1 chip according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Cusson_G1
|
| Data processing |
Sequencing reads were assessed for quality with FastQC (v0.11.5) (Andrews, 2019).
Sequences were trimmed for adapters, quality, and minimum length with Trimmomatic (v0.36) (Bolger et al., 2014).
The existing annotations from the draft genome were augmented by merging them with the read mapping information from all samples using StringTie prior to counting reads at each locus with featureCounts (v2.0.0, counting gene_id meta-features) (Liao et al., 2014).
Statistical analyses were conducted with the DESeq2 package (v1.28.1) (Love et al., 2014) in R (v4.0.2) (R Core Team, 2020), using the apeglm package (v1.10.0) (Zhu et al., 2019) for shrinkage estimation.
Data in this GEO submission report the normalized counts after variance stabilizing transformation with vst(fitType='local') within DESeq2.
Genome_build: lda.genome.v0.3.fasta available here: https://doi.org/10.17605/OSF.IO/UNZ2V
Supplementary_files_format_and_content: PROJECT_Cusson_pupae_flight_vst_counts.txt: Normalized count data after variance-stabilizing transformation.
Supplementary_files_format_and_content: The 'PROJECT_Cusson_pupae_flight_representative_transcripts.fa' contains a representative transcript sequence for each locus in the genome for which gene-level expression levels are reported. The best representative at each locus was chosen based upon the highest expression of the various splice variants from StringTie, counting transcript_id meta-features.
|
| |
|
| Submission date |
Sep 23, 2020 |
| Last update date |
Jun 03, 2024 |
| Contact name |
Christopher Ian Keeling |
| Organization name |
Natural Resources Canada
|
| Department |
Canadian Forest Service
|
| Lab |
Laurentian Forestry Centre
|
| Street address |
1055 rue du PEPS
|
| City |
Quebec City |
| State/province |
QC |
| ZIP/Postal code |
G1V 4C7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL29179 |
| Series (1) |
| GSE158466 |
Spongy moth gene expression during female pupal development |
|
| Relations |
| BioSample |
SAMN16213549 |
| SRA |
SRX9152884 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
