|
| Status |
Public on Jun 29, 2022 |
| Title |
SG2-R1 |
| Sample type |
SRA |
| |
|
| Source name |
larval salivary gland
|
| Organism |
Inopus flavus |
| Characteristics |
group: Exposed to plant root
|
| Treatment protocol |
The larval body surfaces were disinfected by soaking in 75% Ethanol for 30s and then rinsing in phosphate-buffered saline (PBS) before dissecting out the salivary glands. The salivary glands (SG) were extracted by pulling out the head capsule and removing all other tissues, such as fat body droplets. The SG tissue from 20 larvae (representing one biological replicate) were pooled together and transferred to Qiazol lysis reagent for RNA extraction.
|
| Growth protocol |
Soldier fly (Inopus sp. near falvus) larvae were collected from an infested sugarcane field near Hay Point, Queensland (21°18' 5"S, 149 °14' 7"E). In February 2018, stools were dug from the ground and large larvae were manually collected from the roots and associated soil. Larvae were transferred to aerated 480 ml polypropylene containers with soil collected from the same sugarcane field and transported to the laboratory and used in experiments within 2 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiazol (R) was used for RNA extraction according to manufacture instruction (QIAGEN; Cat No.: 79306). The RNA samples were treated with DNase I for 1 h at 37°C and then their concentrations were measured using a spectrophotometer and integrity was ensured through analysis of RNA on a 1% (w/v) agarose gel.
The PCR-based cDNA libraries were prepared using the illumine TrueSeq cDNA library construction kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The CLC Genomics Workbench version 11.01 was used for bioinformatics analyses. All libraries were trimmed from any vector or adapter sequences remaining. Low quality reads (quality score below 0.05) and reads with more than two ambiguous nucleotides were discarded.
The genome sequence of this species is not available and we used de novo assembly to process this data. The contigs arising from the de novo assembly were used as a reference set of transcripts for RNAseq analysis. Short-read sequence data from the SG of root-exposed and control (starved) larvae was separately mapped against the reference set of assembled transcripts using the CLC Genome Workbench RNAseq function (min. length fraction=0.9, maximum mismatches=2).
The relative expression levels were output as RPKM (Reads Per Kilobase of exon model per Million mapped reads) values, which considers the relative size of the transcripts and only uses the mapped-read datasets (i.e. it excludes the non-mapped reads) to determine relative transcript abundance.
To explore the differential expression profile between two groups of samples in CLC genomic workbench, each gene is modelled by a separate Generalized Linear Model (GLM). The use of the GLM formalism allows the fitting of curves to expression values without assuming that the error on the values is normally distributed. The Wald Test was also used to compare each sample against its control group to test whether a given coefficient is non-zero. We considered genes with more than 2-fold changes and a false discovery rate (FDR) of less than 0.05 as significantly modulated genes.
|
| |
|
| Submission date |
Mar 01, 2019 |
| Last update date |
Jun 29, 2022 |
| Contact name |
Kayvan Etebari |
| E-mail(s) |
k.etebari@uq.edu.au
|
| Organization name |
The University of Queensland
|
| Department |
School of Biological Sciences
|
| Lab |
Insect host-pathogen Interaction
|
| Street address |
Building No 8
|
| City |
St Lucia |
| State/province |
QLD |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
|
| Platform ID |
GPL30310 |
| Series (1) |
| GSE127658 |
Australian sugarcane soldier fly’s salivary gland transcriptome in response to starvation and feeding on sugarcane crops |
|
| Relations |
| BioSample |
SAMN11055541 |
| SRA |
SRX5465653 |
