|
| Status |
Public on Aug 01, 2016 |
| Title |
Waite population 1 |
| Sample type |
SRA |
| |
|
| Source name |
Waite population_Larvae
|
| Organism |
Plutella xylostella |
| Characteristics |
population: South Australia (Waite)
tissue: whole larval body
developemental stage: 3rd instar Larvae
|
| Treatment protocol |
No Treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fifteen 3rd instar larval samples using Triazol® following the manufacturer’s protocol (Life Technologies).
The small RNA libraries were generated from both populations with three biological replicates using the Illumina Truseq small RNA preparation kit at the Australian Genome Research Facility (AGRF-Melbourne, Australia). The purified cDNA libraries were sequenced on Illumina HiSeq and raw sequencing reads (50 nt) were obtained using Illumina’s Sequencing Control Studio software.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The quality of raw data from each library was controlled by CLC Genomic Workbench version 7.5.1. Raw data were stripped of adapters and reads with quality score above 0.05 and less than 2 ambiguous nucleotides were retained. Reads without 3’ adapters and also reads with less than 16 nt were discarded from the libraries. Clean data considered as mappable reads for further analysis.
Tab separated files with the read sequences and their counts were used as input file for novel and homologous miRNA analysis using sRNAtoolbox. Although sRNAtoolbox is a powerful tool for novel miRNA identification, all predicted miRNAs were then individually inspected for their pre-miRNA secondary structure, mature miRNA position on the stem loop, and their abundance in our libraries. We also double-checked their possible similarity with other RNA sequences (such as tRNA and rRNA) in Rfam
We also Used CLC genomic workbench to produce pxy-miRNA profile
Genome_build: The first assembly of P. xylostella genome (GCA_000330985.1) was used
Supplementary_files_format_and_content: text file, miRNA copy number
|
| |
|
| Submission date |
Dec 23, 2015 |
| Last update date |
May 15, 2019 |
| 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 |
GPL17076 |
| Series (1) |
| GSE76321 |
Revised annotation of Plutella xylostella microRNAs |
|
| Relations |
| BioSample |
SAMN04366488 |
| SRA |
SRX1501867 |
