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| Status |
Public on Jun 17, 2024 |
| Title |
Dmel pupae P1 3 |
| Sample type |
SRA |
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| Source name |
whole body
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole body
replicate: biol rep 3
gender: unknown
developmental stage: pupae
timing: P1
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| Growth protocol |
The flies, spanning all developmental stages, were reared on the standard Drosophila wheat meal-yeast-sugar-agar medium and maintained at a constant temperature of 25°C.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The samples underwent a thorough rinsing process to remove any residual food and yeast, using the PBS buffer. Following this step, total RNA was extracted from the samples using RNAzol RT reagent (MRC, Cincinnati, OH, USA), following the manufacturer’s recommended protocols. RNA quality assessments were performed through gel electrophoresis, and the RNA samples were carefully stored in ethanol at -70°C, in preparation for subsequent experimental procedures.
Ribosomal RNA depletion was conducted using the NEBNext® Poly(A) mRNA Magnetic Isolation Module. Subsequently, RNA library preparation was carried out with the NEBNext® Ultra™ II Directional RNA Library Prep Kit, and the prepared libraries were sequenced on the Illumina HiSeq4000 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
pupae P1 3
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| Data processing |
Low-quality nucleotides and reads were systematically eliminated using the fastp tool with the default parameters. Subsequently, the filtered reads were aligned to the respective reference genomes with the kallisto pseudomapping procedure and the BDGP6.46 and DvirRS2 assemblies as references for D. melanogaster and D. virilis, respectively.
Assembly: BDGP6.46 for D. melanogaster and DvirRS2 for D. virilis
Supplementary files format and content: {species}_vst_matrix.csv files contain comma-separated table witth normalized expression values for each sample and each replicate.
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| Submission date |
Jun 14, 2024 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Aleksandra M Ozerova |
| E-mail(s) |
alexapogorelskaya@gmail.com
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| Phone |
+79164171135
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| Organization name |
Skolkovo Institute of Science and Technology
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| Department |
Life sciences
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| Street address |
Skolkovo Innovation Center, Bolshoy Boulevard, 30, p.1
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| City |
Moscow |
| ZIP/Postal code |
121205 |
| Country |
Russia |
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| Platform ID |
GPL21306 |
| Series (1) |
| GSE269951 |
Temporal dynamics of gene expression during metamorphosis in two distant Drosophila species |
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| Relations |
| BioSample |
SAMN41846184 |
| SRA |
SRX24935403 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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