|
| Status |
Public on May 10, 2024 |
| Title |
SG-UPF1KD-3 |
| Sample type |
SRA |
| |
|
| Source name |
Salivary Glands
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Salivary Glands
genotype: w; UAS-UPF1RNAi/+; FkhGAL4
|
| Growth protocol |
Flies grown at 25 degrees celcius on standard cornmeal food
|
| 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. 1 µg of RNA was used for library construction and sequencing.
Poly(A) RNA was enriched from total RNA using NEBNext Poly(A) Magnetic Isolation Module (New England Biolabs E7490L). Libraries constructed using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolab E7420L), and NEBnext Multiplex Oligos for Illumina Dual Index Primers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequences trimmed using TRIMMOMATIC PE (v.39)
Sequences aligned to Dm6.56 using HISAT2 (v2.2.1)
SAMtools (v1.19.2) to sort and convert sam files to BAM files
HTSeq (v0.13.5) 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 |
Apr 29, 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 |
GPL21306 |
| Series (1) |
| GSE266138 |
UPF1 is required for gene expression in mitochondria and for the elimination of paternal mtDNA |
|
| Relations |
| BioSample |
SAMN41117250 |
| SRA |
SRX24399814 |
