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Sample GSM5380608 Query DataSets for GSM5380608
Status Public on Dec 31, 2023
Title Wing disc_AIDUbAux_replicate 2
Sample type SRA
 
Source name Wing discs
Organism Drosophila melanogaster
Characteristics genotype: ub> Med19AID
auxin treatment: yes
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 Med19 degradation (drived by ub driver)
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 SAMN19693938
SRA SRX11137392

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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