|
| Status |
Public on Jun 15, 2023 |
| Title |
2-4h embryo shHDAC3 Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole embryo
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Whole embryo
genotype: tub-GAL4/shRNA HDAC3
developmental stage: 2-4h after egg laying
treatment: HDAC3 shRNA
|
| Growth protocol |
Embryos were grown at 25°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were homogenized in 300 µL TRIzol LS Reagent followed by total RNA purification using the Direct-zol RNA MiniPrep kit (R2050, ZymoResearch).
RNA libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
usegalaxy.eu
RNA-seq reads were mapped to the Drosophila melanogaster (dm6) genome assembly using STAR with default parameters. RNA-seq count tables were generated with featureCounts and differential expression analysis (DE) of HDAC3 shRNA vs. Control, shRNA-resistant rescueWT, shRNA-resistant rescueY303F, shRNA-resistant rescueK26A or shRNA-resistant rescueHEBI was performed using DEseq2.
Assembly: dm6
Supplementary files format and content: xlsx file for RNA-seq count table
|
| |
|
| Submission date |
Jun 16, 2022 |
| Last update date |
Jun 15, 2023 |
| Contact name |
Mattias Mannervik |
| E-mail(s) |
[email protected]
|
| Organization name |
Stockholm University
|
| Street address |
Svante Arrhenius väg 20C
|
| City |
Stockholm |
| ZIP/Postal code |
10691 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE206247 |
Separation of transcriptional repressor and activator functions in HDAC3 [RNA-Seq] |
| GSE206249 |
Separation of transcriptional repressor and activator functions in HDAC3 |
|
| Relations |
| BioSample |
SAMN29135690 |
| SRA |
SRX15720270 |
