|
| Status |
Public on Jul 05, 2020 |
| Title |
D_simulans |
| Sample type |
SRA |
| |
|
| Source name |
Johnston's Organ
|
| Organism |
Drosophila simulans |
| Characteristics |
tissue: Johnston's Organ
age: Adult
reference genome annotation: D.simulans 1.4
|
| Growth protocol |
All flies were raised at 25˚C on standards fly food
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNAqueous micro kit (Ambion)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Normalized_across_species.txt
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, then mapped to their respective genomes using tophat2 v 2.0.3 (default parameters)
HT-Seq count (option -str=no) was used to count the number of reads falling within each species exonic regions.
RPKM values were calculated for each sample independetly .
Ensembl GeneTreess 2013 was used to obtain orthology relationships across Drosophila species
Normalization across one-to-one orthologous regions was performed using the upper-quantile methodology.
Genome_build: D.melanogaster 5.46; D.persimilis 1.3; D.pseudoobscura 2.30; D.simulans 1.4; D.yakuba 1.3
Supplementary_files_format_and_content: tab-delimited text files include htseq counts for each sample and normalized values for one-to-one orthologs across the Drosophila species under study.
|
| |
|
| Submission date |
Jul 05, 2017 |
| Last update date |
Jul 05, 2020 |
| Contact name |
Stein Aerts |
| Organization name |
KULeuven
|
| Department |
Center for Human Genetics
|
| Lab |
Laboratory of Computational Biology
|
| Street address |
Herestraat 49
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL13306 |
| Series (1) |
| GSE100837 |
Comparative transcriptomics in the Drosophila Auditory Organ |
|
| Relations |
| BioSample |
SAMN07325981 |
| SRA |
SRX2986132 |
