|
| Status |
Public on Mar 20, 2020 |
| Title |
Unmodified rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole fly
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole fly
genotype: w1118
food: unmodified holidic
|
| Treatment protocol |
Adult male flies were raised on either unmodified or glucose-enriched (50 g/L) holidic food for 20 days at 25˚C.
|
| Growth protocol |
Flies were raised on standard cornmeal at 25˚C before eclosion.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. 5 whole flies were used per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Base calls performed using Cyberduck(FTP).
FASTQC was used to evaluate the quality of raw paired-end sequencing reads.
Adaptors and reads of less than 36 base pairs in length were trimmed from the raw reads using Trimmomatic.
Reads were aligned to the Drosophila transcriptome- bdgp6 with HISAT2 (version 2.1.0).
The resulting BAM files were converted to SAM flies using Samtools (version 1.8).
The converted files were counted using Rsubread (version 1.24.2) and loaded into EdgeR.
In EdgeR, genes with counts less than 1 count per million were filtered and libraries were normalized for size. Normalized libraries were used to call genes that were differentially expressed among treatments.
Genome_build: Drosophila transcriptome- bdgp6
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample, and differentially expressed genes
|
| |
|
| Submission date |
Mar 19, 2020 |
| Last update date |
Mar 20, 2020 |
| Contact name |
Edan Foley |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Alberta
|
| Department |
Medical Microbiology and Immunology
|
| Street address |
114 ST and 87 AVE
|
| City |
Edmonton |
| State/province |
Alberta |
| ZIP/Postal code |
T6G 2E1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL23323 |
| Series (1) |
| GSE147222 |
Expression data from D. melanogaster raised on glucose-enriched or unmodified holidic food |
|
| Relations |
| BioSample |
SAMN14404425 |
| SRA |
SRX7952481 |
