|
| Status |
Public on Jul 26, 2021 |
| Title |
Vitamin A- 1 |
| Sample type |
SRA |
| |
|
| Source name |
Vitamin A-_whole head
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain/genotype: Wild type Canton S
treatment: vitamin A deprived
age: four day old
gender: female
tissue: Whole head
|
| Treatment protocol |
Flies were raised on food with or without beta-carotene.
|
| Growth protocol |
Flies were raised on minimal food with or without addition of beta-carotene, inside incubators set at 25°C temperature and 50% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from heads of four day old female flies using Trizol followed by Qiagen Rneasy protocol.
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 |
M018_AACCAG
|
| Data processing |
Raw reads were processed for quality control using fastqc (v.0.11.5)
Raw reads were trimmed using Trim Galore (v0.4.2)
Raw reads were aligned to dmel genome (r6.24, flybase.org ) using STAR (v2.5.3a)
Gene level read counts was produced by featureCounts from Subread (v1.6.2) package
Genome_build: r6.24, flybase.org
Supplementary_files_format_and_content: gene level read raw count (abundance measurements)
|
| |
|
| Submission date |
Jun 23, 2021 |
| Last update date |
Jul 27, 2021 |
| Contact name |
Jens Rister |
| E-mail(s) |
Jens.Rister@umb.edu
|
| Organization name |
University of Massachusetts Boston
|
| Department |
Biology
|
| Lab |
RISTER LAB
|
| Street address |
100 Morrissey Boulevard
|
| City |
Boston |
| State/province |
MASSACHUSETTS |
| ZIP/Postal code |
02125 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE178712 |
Vitamin A deficiency affects gene expression in the Drosophila melanogaster head |
|
| Relations |
| BioSample |
SAMN19826559 |
| SRA |
SRX11204010 |
