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Series GSE110240 Query DataSets for GSE110240
Status Public on Feb 01, 2019
Title Title: Transcriptional profiles (mRNA-seq) of Drosophila G9aDD1 mutants and control during 0, 6 and 12 hours of paraquat oxidative stress exposure.
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Investigating the role of Drosophila G9a in oxidative stress responses.
Methods: Flies were collected after eclosion and allowed to recover from CO2 exposure for 5 days prior to paraquat exposure. Paraquat (Methyl viologen dichloride hydrate 98 %; Sigma 856177) was mixed into the flyfood at 40 °C to a final concentration of 50 mM. For OS induction, 5-9 day old flies were transferred to paraquat containing food and incubated at 25 °C and 70 % humidity. At each time point, flies were flash frozen in liquid nitrogen followed by vortexing and filtering through a series of sieves to isolate heads from other body parts. 200 fly heads per sample were used for RNA extraction using QIAGEN lipid mini tissue kit. The TruSeq RNA Sample Preparation Kit v2 (Illumina) was used to prepare adapter ligated PCR fragments for sequencing. PCR was used to selectively enrich the fragments containing the adapters. The PCR fragments were validated using Agilent 2200 TapeStation. Single indexed samples were multiplexed and sequenced on an Illumina HiSeq 2000 sequencing system (Illumina) in single-end mode with a read length of 35 bp. Quality of sequenced reads was assessed with FastQC. The RNAseq experiments were conducted on two biological duplicates for each condition. Sequenced reads were aligned with Burrows-Wheeler algorithm (BWA) (Li & Durbin, 2010) to the Drosophila reference genome (BDGP.5, and per gene read counts were generated with HTSeq count (Anders et al, 2015). 25–30 million reads with high quality alignment were obtained for each sample and used for differential expression analysis. DESeq (Anders & Huber, 2010) was used to obtain library size-normalized read counts and to calculate differential expression of genes in 4 pairwise comparisons: 0 h versus 6 h and 0 h versus 12 h after OS in both G9a mutants and controls (fold change ≥1.5, adjusted p-value≤ 0.05, Benjamini-Hochberg).
Results: We found 2731 genes to be differential expressed in at least one of the four pairwise comparisons. The largest group of differentially expressed (DE) genes are highly augmented upon OS induction in the G9a mutant (41.7 % of all DE genes). The second largest group of DE genes (23.9 % of all DE genes) were more downregulated in G9a mutant in response to OS. Genes that are over-activated in G9a mutants are predominantly involved in OS response and OS mediated damage, whereas genes that are downregulated in G9a mutants are involved in energy metabolism.
Conclusions: Our data suggest that G9a provides an epigenetic mechanism that safeguards an appropriate transcriptional response to OS and preserves immediately available energy, thereby acting as a critical regulatory hub between the transcriptional and physiological responses to oxidative stress.
Overall design fly-head mRNA libraries of 5-9 days old male G9aDD1 mutant and control during 0, 6 and 12 hours of paraquat oxidative stress exposure were sequenced in duplicate on Hi-seq 2000.
Contributor(s) Riahi H, Kramer JM, Schenck A
Citation(s) 30860988, 34030685
Submission date Feb 06, 2018
Last update date Jun 03, 2021
Contact name Human Riahi Asl
Phone 0031619898485
Organization name Radboud UMC
Department Human Genetics
Lab Drosophila model of brain disorders
Street address Geert Grooteplein Zuid 10
City Nijmegen
State/province Gelderland
ZIP/Postal code 6525 GA
Country Netherlands
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (12)
GSM2983102 wt control 0 hours OS 1
GSM2983103 wt control 0 hours OS 2
GSM2983104 wt control 6 hours OS 1
BioProject PRJNA433235
SRA SRP132308

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Supplementary file Size Download File type/resource
GSE110240_mt0VSmt12.txt.gz 103.2 Kb (ftp)(http) TXT
GSE110240_mt0VSmt6.txt.gz 58.0 Kb (ftp)(http) TXT
GSE110240_normalized_HTseq_count_data.txt.gz 800.9 Kb (ftp)(http) TXT
GSE110240_wt0VSwt12.txt.gz 44.0 Kb (ftp)(http) TXT
GSE110240_wt0VSwt6.txt.gz 30.2 Kb (ftp)(http) TXT
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