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ABSTRACT: RNA sequencing on CG4928 knockdown flies

PROVIDER: PRJNA663443 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12641461.fastq.gz	Fastqsanger.gz
	SRR12641462.fastq.gz	Fastqsanger.gz
	SRR12641463.fastq.gz	Fastqsanger.gz
	SRR12641464.fastq.gz	Fastqsanger.gz
	SRR12641465.fastq.gz	Fastqsanger.gz

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Project description:To test whether other genes were being silenced in the Cyp6g1 knockdown strain due to off-target RNAi effects, and whether other gene expression changes were contributing to the altered susceptibility to imidacloprid in these knockdown flies. A comparison between w;Act5C-GAL4/CyO; UAS:RNAi_Cyp6g1Hp2/TM3Sb and the genetic control w;Act-GAL4/CyO;+/TM3Sb was performed. Ten 2-3 day old adult males or females were transferred to sugar-agar plates and then collected at various time points (0, 2, 5, 8 hours). The RNA samples for up to three independent experiments per timepoint for each genotype were then pooled, in equal concentrations, before hybridisation to the Affymetrix Drosophila GeneChip 1. As a preliminary analysis provided evidence for assuming that there is no interaction between genotype and duration in the sugar-agar plate, the knockdown and control chips for each of the five timepoints provided some degree of replication for the comparison between the knockdown flies and control flies. Differential expression that was consistently observed between knockdown and control over each of the five timepoints was regarded as providing evidence of a genuine difference. 2-3 day old adult flies of the appropriate genotype (Cyp6g1 knockdown or its genetic control) were transferred to bioassay plates and collected after specified timepoints in the assay plate, i.e. 0, 2, 5 or 8 hours. Each experiment contained ?3 replicates of each genotype/timepoint, and a different number of independent experiments (1-3) were pooled per microarray sample as described below. An experiment is defined as treatments set up from the same cohort of flies on a single day. Independent experiments are set up using distinct cohorts of flies, on distinct days. We included one pair of tests to compare samples from single experiments with pooled samples from independent experiments (DS003001 to DS003004, DS003002 to DS003005), and also a single pair of samples to compare males to females (DS003002 to DS003003). As it turned out - in our analysis - the timepoints selected were not discriminative, in that there were no differences detected that could be attributed to an effect of time in the bioassay.

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