|
| Status |
Public on Jul 04, 2014 |
| Title |
UP09003135 |
| Sample type |
SRA |
| |
|
| Source name |
UP_Thorax
|
| Organism |
Melitaea cinxia |
| Characteristics |
population: UP
gender: Female
|
| Treatment protocol |
The material was collected in the autumn of 2009 as diapausing larvae from four different regional populations in northern Europe: Åland (Finland), Saaremaa (Estonia), Uppland (Sweden) and Öland (Sweden). The larvae overwintered in mixed (within population) groups in a growth chamber under constant temperature of +5°C and 85% relative humidity. In spring 2010, larvae were reared singly under common garden conditions (12:12; L/D; 28/15°C) with fresh leaves of the host plant Plantago lanceolata. After eclosion the adults were held in the same common garden conditions for three days.
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Illumina Casava 1.7 and 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.
Genewise read counts were normalized using TMM method in R package edgeR. Normalized counts were obtained by dividing unnormalized counts by effective library size.
Genome_build: GenBank APLT01000000 (submitted)
Supplementary_files_format_and_content: text file including unnormalized read counts of 16667 genes is linked to each sample records and 'NormalizedCounts.txt' is linked to Series records.
|
| |
|
| Submission date |
Jun 06, 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 |
GPL17256 |
| Series (1) |
| GSE47692 |
Genomic variation and adaptation in fragmented landscapes |
|
| Relations |
| BioSample |
SAMN02191887 |
| SRA |
SRX306917 |
