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Series GSE213325 Query DataSets for GSE213325
Status Public on Jan 31, 2024
Title Xrp1 governs the stress response program to spliceosome dysfunction
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Unperturbed pre-mRNA splicing is crucial for proper expression of eukaryotic genes, but also maintenance of genome integrity. Loss of splicing factors is associated to DNA damage arising through different mechanisms, among which is the accumulation of mutagenic DNA/RNA hybrids (R-loops). RNase H1 recognizes and degrades the RNA moiety within R-loops, and is a commonly used marker for R-loops. Ecdysoneless protein was previously shown to participate in pre-mRNA splicing through its association with the U5 snRNP. In this study we have performed in vivo Targeted DamID using the Dam-RNase H1 construct to map the localization of R-loops throughout the Drosophila genome in control and Ecd-deficient Drosophila wing imaginal discs. 
 
Overall design Low-level expression of UAS-LT3-Dam (noise control) and UAS-LT3-Dam-RNase H1 (binding signals) was performed in wing imaginal discs (WDs) of Drosophila third instar larvae in control animals and temperature-sensitive ecd1 mutants. Heat-sensitive tub-Gal80 prevented the expression of the Dam constructs at 25 °C at which the larval tissues were developing. The larvae were heat shocked at 29 °C for 24 hours prior to dissection on day 7 after egg laying. The heat shock simultaneously enables the transcription of the Dam constructs, and abolishes the function of the mutant ecd1 protein. The WDs were dissected, processed according to established Targeted DamID protocols and the derived material sequenced in three biological replicates. 
Web link https://doi.org/10.1093/nar/gkae055
 
Contributor(s) Stankovic D, Tain LS, Uhlirova M
Citation(s) 38303573
Submission date Sep 14, 2022
Last update date Apr 02, 2024
Contact name Mirka Uhlirova
E-mail(s) mirka.uhlirova@uni-koeln.de
Organization name CECAD Research Center Cologne
Department Institute for Genetics
Lab Uhlirova Lab
Street address Joseph-Stelzmann Str. 26
City Cologne
State/province NRW
ZIP/Postal code 50931
Country Germany
 
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (8)
GSM6578990 nub>Dam control
GSM6578991 nub>Dam-RNase H1 replicate 1
GSM6578992 nub>Dam-RNase H1 replicate 2
Relations
BioProject PRJNA880539

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE213325_Supplementary_Dataset_6_Dam-RNase_H1_Peaks.xlsx 1.2 Mb (ftp)(http) XLSX
GSE213325_Supplementary_Dataset_6a_unique_gene_results_RNH_ctrl_peaks.txt.gz 142.2 Kb (ftp)(http) TXT
GSE213325_Supplementary_Dataset_6b_unique_gene_results_for_ecd1_peaks.txt.gz 152.5 Kb (ftp)(http) TXT
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Processed data are available on Series record

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