GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM8330956 Query DataSets for GSM8330956
Status Public on Jun 17, 2024
Title Dmel pupae P3 2
Sample type SRA
Source name whole body
Organism Drosophila melanogaster
Characteristics tissue: whole body
replicate: biol rep 2
gender: unknown
developmental stage: pupae
timing: P3
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.
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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description pupae P3 2
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.
Submission date Jun 14, 2024
Last update date Jun 17, 2024
Contact name Aleksandra M Ozerova
Phone +79164171135
Organization name Skolkovo Institute of Science and Technology
Department Life sciences
Street address Skolkovo Innovation Center, Bolshoy Boulevard, 30, p.1
City Moscow
ZIP/Postal code 121205
Country Russia
Platform ID GPL21306
Series (1)
GSE269951 Temporal dynamics of gene expression during metamorphosis in two distant Drosophila species
BioSample SAMN41846179
SRA SRX24935408

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap