|
| Status |
Public on Nov 09, 2022 |
| Title |
wt_for_comparison_with_SceI48A_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Stage 16 single embryo
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Stage 16 single embryo
genotype: wt
|
| Growth protocol |
Drosophila embryos were grown on standard medium at 25˚C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single Drosophila embryos of the desired genotypes were collected and disrupted in 1 mL of Trizol (ThermoFisher Scientific) complemented bwith 8 µg of UltraPure glycogen (ThermoFisher Scientific). Purification of total RNA was performed according to instructions accompanying the Trizol reagent.
Libraries were prepared according to Illumina's instructions using a polyA enrichment step.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read quantification was performed from fastq files using Salmon (Patro et al., 2017).
Abundances were summarized from transcript- to gene-level with the Bioconductor package Tximeta (Love et al., 2020).
Differential expression analysis was performed using the DESeq2 package (Love et al., 2014)
PCA analysis was used to select datasets from wild-type and mutant embryos of the same developmental stage.
Assembly: dm6
Supplementary files format and content: Bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).
Supplementary files format and content: Two tables (1 for the comparison between wt and Asx0 mutants and 1 for the comparison between wt and SceI48A mutants) containing differential gene expression information from DESeq2 (Love et al., 2014).
|
| |
|
| Submission date |
Aug 01, 2022 |
| Last update date |
Nov 09, 2022 |
| Contact name |
Jürg Müller |
| Organization name |
Max Planck Institute of Biochemistry
|
| Street address |
Am Klopferspitz
|
| City |
Martinsried |
| State/province |
Bavaria |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE210235 |
PR-DUB preserves Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of nucleosome stacking (RNA-Seq) |
| GSE210236 |
PR-DUB preserves Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of nucleosome stacking |
|
| Relations |
| BioSample |
SAMN30081822 |
| SRA |
SRX16752241 |
