|
| Status |
Public on May 10, 2024 |
| Title |
S2-WT-1 |
| Sample type |
SRA |
| |
|
| Source name |
S2 cell
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2 cell
genotype: WT
|
| Growth protocol |
Cells grown at 27 degrees celcius, in Schneider's Insect Cell Media, supplemented with Fetal Bovine Serum and antibotics (Penicillin and Streptomycin)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol. The upper phase was taken, and RNA was precipitated. Precpitated RNA was dissolved in dH2O.
Library was constructed by Novogene, following polyA enrichment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Description |
instrument model: Illumina NovaSeq X Plus
|
| Data processing |
Sequences trimmed using TRIMMOMATIC PE
Sequences aligned to Dm6.56 using HISAT2
SAMtools to sort and convert sam files to BAM files
HTSeq to calculate raw counts from bam files
DESeq2 for differential expression analysis
Assembly: Dm6.56 FlyBase (https://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.56_FB2024_01/)
Supplementary files format and content: Raw gene counts in plain .txt files, annotated with FlyBase Gene ID
|
| |
|
| Submission date |
May 07, 2024 |
| Last update date |
May 10, 2024 |
| Contact name |
Matthew Wright |
| E-mail(s) |
MTW728@student.bham.ac.uk
|
| Organization name |
University of Birmingham
|
| Department |
School of Biosciences
|
| Street address |
Edgbaston
|
| City |
Birmingham |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL34457 |
| Series (1) |
| GSE266138 |
UPF1 is required for gene expression in mitochondria and for the elimination of paternal mtDNA |
|
| Relations |
| BioSample |
SAMN41253845 |
| SRA |
SRX24485335 |
