 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 19, 2020 |
| Title |
Rp_H_4M_04 |
| Sample type |
SRA |
| |
|
| Source name |
Central Nervous System CNS
|
| Organism |
Rhagoletis pomonella |
| Characteristics |
host: Hawthorn Tree
diapause age: 4 Months diapause
location: USA: Urbana Illinois
lifestage: Pupa
collection year: 2014
|
| Growth protocol |
Infested apple and hawthorn fruits were collected from Urbana, IL in the late summer and fall of 2014. Infested fruit were returned to the laboratory at the University of Florida, emerging larvae were collected and held at ~24C 14:10 LD for 10 days to complete pupation and enter diapause, then pupae were transferred to 3.5C at 95% Relative Humidity (RH). At monthly intervals from 2 to 6 months we dissected out the Central Nervous System (CNS), homogenized pools of 10 CNS, and extracted RNA (5 samples per time point per host). RNA sequencing libraries were prepared using Illumina’s tru-seq stranded mRNA kit and sequenced using 100bp single end Illumina HiSeq 2500. Cleaned reads were mapped to the R. zephyria genome using STAR, and read counts were generated using RSEM.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Flies were disected and CNS removed, extractions consisted of pools of 10 fly CNS, RNA extraction
Illumina mRNA tru-seq stranded
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Pool of 10 CNS
|
| Data processing |
Reads were mapped to the Rhagoletis zephyria genome using STAR
Read counts were estimated in RSEM
Genome_build: NCBI Assembly: GCA_001687245.1, Rhagoletis_zephyria_1.0
Supplementary_files_format_and_content: RSEM output file - counts per gene
|
| |
|
| Submission date |
Nov 15, 2019 |
| Last update date |
Aug 20, 2020 |
| Contact name |
Eddy Dowle |
| E-mail(s) |
eddy.dowle@otago.ac.nz
|
| Organization name |
University of Otago
|
| Department |
Department of Anatomy
|
| Street address |
270 Gt King St
|
| City |
Dunedin |
| ZIP/Postal code |
9016 |
| Country |
New Zealand |
| |
|
| Platform ID |
GPL27760 |
| Series (1) |
| GSE140473 |
Genome-wide variation and transcriptional changes in diverse developmental processes underly the rapid evolution of seasonality |
|
| Relations |
| BioSample |
SAMN13293279 |
| SRA |
SRX7157133 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4162667_Rp_H_4M_04_CGCTCATT-ATAGAGGC_L002_.rsem.genes.results.txt.gz |
437.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
