|
| Status |
Public on Apr 07, 2020 |
| Title |
deletion CBS(5) [C5FT1] |
| Sample type |
SRA |
| |
|
| Source name |
deletion CBS(5)_thorax
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: CBS(5)
Sex: Female
age: 5-day old
tissue: thorax
|
| Treatment protocol |
No treatment were performent in this experiment
|
| Growth protocol |
Flies (separately males and females) were maintained at 23°C on standard yeast, sugar, and agar medium in 40 ml vials at a density of 20 flies per vial throughout the experiment. All flies were synchronized by age: enclosing individuals were collected daily, transferred to new vials with medium, and then aged appropriately
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from 5 days male and female flies: control line-58492, CBS lines-CBS5 and CBS8, CSE1, MST15, with double deletion CBS5 /CSE1, and CBS8 /CSE1 using RNAzol RT according to the manufacturer's protocol. RNA quality was assessed using an Agilent 2100 Bioanalyzer instrument (Agilent Technologies, USA) using the Agilent RNA 6000 nano Kit (Agilent Technologies). The concentration of RNA samples was evaluated on a Qubit 2.0 Thermo fluorimeter (Fisher Scientific)
Libraries were prepared from 1000 ng of total RNA using the NEBNext® Ultra ™ II Directional RNA Library Prep Kit for Illumina (NEB, UK) according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
short read quality assesment using fastqc
read trimming with trimmomatic ver. 0.38
Splice-aware short read alignment with STAR (ver 2.5.0a)
exonic read counting using featureCounts package (ver 1.5.0-p1)
Genome_build: Drosophila melanogaster BGP6
Supplementary_files_format_and_content: processed files are tab-separated files with Flybase gene ID (1 column) and non-normalized read number in gene (2 column)
|
| |
|
| Submission date |
Apr 06, 2020 |
| Last update date |
Apr 09, 2020 |
| Contact name |
Alexander Pertovich Rezvykh |
| E-mail(s) |
[email protected]
|
| Organization name |
Engelhardt Molecular Biology Institute
|
| Department |
Russian Academy of Sciences
|
| Lab |
Laboratory of molecular mechanisms of biological adaptation
|
| Street address |
Vavilova, 32
|
| City |
Moscow |
| State/province |
Moscow |
| ZIP/Postal code |
119991 |
| Country |
Russia |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE148109 |
The genome-wide transcriptional consequences of the deletions of sulfur metabolism genes in Drosophila melanogaster |
|
| Relations |
| BioSample |
SAMN14543329 |
| SRA |
SRX8062245 |
