|
| Status |
Public on Dec 27, 2014 |
| Title |
vir_cont_1 |
| Sample type |
SRA |
| |
|
| Source name |
whole fly pooled (20)
|
| Organism |
Drosophila virilis |
| Characteristics |
strain: TOY3F9
origin: Toyama, Japan
age: 27 days post-eclosion
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen flies were pooled. RNA was extracted from each sample using Tri Reagent (Sigma-Aldrich) followed by RNeasy Mini kit (Qiagen) purification with DNase treatment.
RNA libraries were prepared for sequencing using standard SOLiD protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Data processing |
trimmed using SOLiD TRIM (with run options: -p 3 -q 22 -y y -e 2 -d 10)
error corrected using SOLiD Accuracy Enhancer Tools (SAET)
trimmed using CLC Genomics Workbench 5.0.1 (quality score: 0.02)
Reads for each sample were mapped individually to the D. virilis genome (r1.2, available from http://flybase.org/) using CLC Bio
HTSeq was used to quantify the read counts mapping uniquely to the reference using the reference annotation available from Flybase (r1.2).
Genome_build: D. virilis genome (r1.2, available from http://flybase.org/)
Supplementary_files_format_and_content: tab-delimited text files of unique read counts mapping to each gene for each sample
|
| |
|
| Submission date |
Jun 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Darren James Parker |
| E-mail(s) |
djp39@st-andrews.ac.uk
|
| Phone |
441334463500
|
| Organization name |
University of St. Andrews
|
| Department |
Centre for Biological Diversity
|
| Street address |
Dyers Brae House
|
| City |
St Andrews, |
| State/province |
Fife |
| ZIP/Postal code |
KY16 9TH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18882 |
| Series (1) |
| GSE58925 |
Transcriptome changes associated with cold acclimation in two species of the Drosophila virilis group |
|
| Relations |
| BioSample |
SAMN02898095 |
| SRA |
SRX641362 |
