 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 01, 2015 |
| Title |
PT11-148-3_650 |
| Sample type |
SRA |
| |
|
| Source name |
Thorax
|
| Organism |
Melitaea cinxia |
| Characteristics |
population: PT
Sex: Female
treatment: Flight1h
|
| Treatment protocol |
Butterflies in treatment group F1 were flash frozen in liquid nitrogen 1 h (average: 62 min, range: 56-69 min) after the beginning of the flight treatment, while butterflies in treatment group F20 were kept overnight in individual 10 x 30 cm cages (08-10 Light/24°C, 10-15 Light/28°C, 15-17 Light/24°C, 17-08 Dark/18°C) with food, and were flash frozen in liquid nitrogen in the following morning, 17-24 hrs (average: 20.5 hrs) after the beginning of the flight treatment. The whole body of the butterfly was preserved, but RNA was extracted only from the thorax. The control group butterflies were treated similarly to the experimental butterflies, with the exception of not experiencing the flight treatment, and were flash frozen 1 hr (C1) or 17-24 hrs (C20) after being moved to the flight treatment conditions. All samples were stored in -80°C until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen butterfly thorax with Trizol (Life Technologies Corporation, CA, USA) followed by chloroform, phenol-chloroform-isoamylalcohol and second chloroform purification. RNA was precipitated with isopropanol and washed with ethanol. RNA quality was verified with NanoDrop measurement (Thermo Fischer Scientific Inc., MA, USA) and Bioanalyzer run (Agilent Technologies, CA, USA).
An in-house strand-specific library construction protocol based on polyA-anchoring. Two libraries with average insertsizes 450nt and 650nt were constructed for each individual.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava 1.8 software used for basecalling.
Reads were trimmed by finding longest subsequence with all bases>=Phred20. PolyA tail was removed and reads with minimum length of 50 bp were mapped with TopHat2 (version 2.0.5) taking into account strand specificity (forward strand).
Mapped read counts were collected within 16667 predicted gene models. Only unique mappings were accepted.
Genewise read counts were normalized using TMM method in R package edgeR. Genes were required to have min.10 reads from min.10 individuals which resulted in 8258 genes.
Genome_build: GenBank APLT01000000
Supplementary_files_format_and_content: Text files include unnormalized read counts of 16667 genes separately for two libraries with different insertsizes. Supplementary file normalizedCounts8258Genes.txt contains TMM-normalized counts where two libraries have been combined for each individual.
|
| |
|
| Submission date |
Jun 13, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Panu Somervuo |
| E-mail(s) |
panu.somervuo@helsinki.fi
|
| Organization name |
University of Helsinki
|
| Street address |
Viikinkaari 4
|
| City |
Helsinki |
| ZIP/Postal code |
00014 University of Helsinki |
| Country |
Finland |
| |
|
| Platform ID |
GPL17255 |
| Series (1) |
| GSE47942 |
Dispersal, flight metabolism and gene expression in the Glanville fritillary butterfly |
|
| Relations |
| BioSample |
SAMN02203589 |
| SRA |
SRX305699 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1162919_PT11-148-3_650.txt.gz |
53.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
