|
| Status |
Public on Jun 04, 2014 |
| Title |
SW_WB01_F1_WF |
| Sample type |
SRA |
| |
|
| Source name |
Pea aphid whole body
|
| Organism |
Acyrthosiphon pisum |
| Characteristics |
genotype: F1
morph: Winged female
age: 2 day old adult
growing conditions: photoperiod L: D cycle = 16:8, temperature 18°C
|
| Treatment protocol |
We collected whole bodies of 30 adult aphids of each of the five morphs and three clones (total of 15 samples) by flash freezing them in liquid nitrogen. Samples were stored at -80°C. We used three different clones as biological replicates
|
| Growth protocol |
For asexual winged and wingless females (photoperiod L: D cycle = 16:8, temperature 18°C), sexual females and males (photoperiod L: D cycle = 13:11 temperature 15°C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using a phenol/chloroform extraction. RNA was quantified by Qubit and the quality was checked by Bioanalyzer (Agilent)
RNA sequencing libraries were constructed per manufacturer instructions with sample-specific tags (Illumina) and sequenced on an Illumina HiSeq 2000 sequence analyzer
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
We mapped sequencing reads to the 36,961 gene predictions of v2.1 annotation of the pea aphid genome (available at aphidbase.com) using the Arraystar Software v.5 (DNAStar Inc.).
Genes with a total raw read count of less than 100 for all 15 libraries were filtered out
The DESeq2 R package was used to normalize the libraries
Genome_build: v2.1 annotation of the pea aphid genome (available at aphidbase.com)
Supplementary_files_format_and_content: .csv file containing gene expression data normalized using DESeq2 R package
|
| |
|
| Submission date |
Apr 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Swapna R. Purandare |
| E-mail(s) |
swapna.purandare@huskers.unl.edu
|
| Organization name |
University of Nebraska-Lincoln
|
| Department |
Biological Sciences
|
| Lab |
Brisson Lab
|
| Street address |
348 Manter Hall
|
| City |
Lincoln |
| State/province |
Nebraska |
| ZIP/Postal code |
68588 |
| Country |
USA |
| |
|
| Platform ID |
GPL18577 |
| Series (1) |
| GSE56830 |
Gene expression profiling of 5 pea aphid morphs |
|
| Relations |
| BioSample |
SAMN02728354 |
| SRA |
SRX518190 |
