|
| Status |
Public on Dec 31, 2023 |
| Title |
Wing disc_AIDUb_replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Wing discs
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: ub> Med19AID
auxin treatment: no
developmental stage: L3 larvae
|
| Treatment protocol |
Female L3 larvae carrying ubiquitin gal4 driver and Med19AID were either fed with Auxin analog NAA (AIDUbAux) for 4h to induce M19 degradation, or not (AIDUb) as a control. A second control was performed to monitor Auxin effect with female Med19AID L3 larvae (without any driver) that were fed with Auxin (AIDAux).There are 3 independant experiments A (samples 1,2,3), B (samples 4,5,6) and C (samples 7,8, 9).
|
| Growth protocol |
Flies were raised at 25°C on standard yeast agar cornmeal medium.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Wing discs were hand-dissected at 4°C RNA extraction was made using TRIzol reagent.
RNA Library was prepared using standard Illumina protocols for strand-specific RNA-seq with PolyA selection.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Control of ub driver effect (no Med19 degradation )
|
| Data processing |
The quality control of fastq sequences was done with FastQC (v0.11.4), then reads were aligned using TopHat2 (v2.0) on the Drosophila melanogaster genome dm6.
Paired reads were counted by gene using htseq (v1.0).
These counts were used to perform differential gene expression analyses using DESeq2 (1.26.0) in R comparing UbAux with either Ub or AID control condition.
We selected differentially expressed genes (DEGs) by setting a significance determined by Benjamini-Hochberg adjusted P-values < 0.05 and -0.5<Log2(FoldChange)<0.5.
Genome_build: dm6
Supplementary_files_format_and_content: The excel file All_DEG_AID.xlsx, contains the matrix table of expressed genes in our samples obtained after the differential analysis by DESeq2.
Supplementary_files_format_and_content: The excel file DEG_UbAuxvsUb_pad0.05_FC0.5.xlsx contains the matrix table obtained after the differential analysis AIDUbAux vs AIDUb by DESeq2 selecting differentially expressed genes with adjusted P-values < 0.05 and -0.5<Log2(FoldChange)<0.5.
|
| |
|
| Submission date |
Jun 14, 2021 |
| Last update date |
Apr 19, 2024 |
| Contact name |
muriel BOUBE-TREY |
| E-mail(s) |
muriel.boube-trey@inserm.fr
|
| Organization name |
CNRS INSERM
|
| Lab |
RESTORE
|
| Street address |
4bis av Hubert Curien
|
| City |
Toulouse |
| ZIP/Postal code |
31100 |
| Country |
France |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE178125 |
Inducible degradation of the Mediator subunit Med19 reveals a dedicated role in the regulation of developmental genes expression |
|
| Relations |
| BioSample |
SAMN19693934 |
| SRA |
SRX11137394 |
