|
| Status |
Public on Oct 01, 2015 |
| Title |
sample_41 |
| Sample type |
SRA |
| |
|
| Source name |
Founder post diapause
|
| Organism |
Bombus terrestris |
| Characteristics |
gender: female
social status: queen
tissue: Eviscerated abdomen with attached fat bodies
age: 4 months
strain: genetic line_141
|
| Treatment protocol |
All queens are mated. Mating was done under lab conditions with unrelated males at the age of 5-10 days. CO2 or diapause treatment were done on the day of mating. mated queens were grouped in a sealed cage and treated with pure CO2 until they were anesthetized (for approximately 1 minute). Queens subsequently were kept in a sealed cage for 30 minutes post treatment and were CO2-treated again 24 hours later. The cage was ventilated between treatments. CO2 treated queens were sampled 24 h or one month post treatment, after they laid eggs and established a colony. In order to induce diapause queens were kept in 4 C for 9-10 weeks. diapausing queens were sampled by the end of the diapause period or were exposed to room temp and daylight and were sampled a month later after they laid eggs and established a colony.
|
| Growth protocol |
Queens were maintained in the laboratory in nest boxes at a constant dark, temperature of 28-30°C and 50% relative humidity, and supplied with unlimited food (50% sucrose and fresh honey-bee collected pollen) during their entire developmental period (except during diapause) until sampling. Diapausing queens were kept in 4 C until sampling
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Queens sampled were flash frozen with dry ice and were immediately transfer to -80°C until further analyses. Eviscerated abdomens with attached fat bodies from individual bees were dissected under dry ice. Total RNA samples were extracted from the abdominal fat bodies using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA quantity and quality were assayed with a ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington DE) and a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Fat body
|
| Data processing |
We removed adaptor sequences, reads composed of more than 5% unknown nucleotides, and reads with more than 20% of the base qualities under 10 using Trimmomatic.
The transcriptome sequencing reads were aligned to the most recent Bombus terrestris genome assembly using Tophat.
The data was normalized using a trimmed mean of M-values (TMM) method.
The DESeq package in R statistical program was used to identify significantly differentially expressed genes.
Genome_build: Bombus terrestris v1.1 (Sadd et al. 2015) ftp://ftp.ncbi.nlm.nih.gov/genomes/Bombus_terrestris/ARCHIVE/BUILD.1.1
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each sample
|
| |
|
| Submission date |
Sep 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Etya Amsalem |
| E-mail(s) |
me.at.isra@gmail.com
|
| Organization name |
Pennsylvania State University
|
| Department |
Entomology
|
| Lab |
Chemical Ecology
|
| Street address |
Orchard Road University Park
|
| City |
State college |
| State/province |
Pennsylvania |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL20914 |
| Series (1) |
| GSE73009 |
Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens |
|
| Relations |
| BioSample |
SAMN04076289 |
| SRA |
SRX1242065 |
