Small RNA expression throughout the development of Drosophila virilis
Ontology highlight
ABSTRACT: Examination of temporal small RNA expression during the embryonic development, larval and adult stages of Drosophila virilis Small RNA sequencing of samples representing different stages of D. virilis development, including eight 2-hour intervals during the first 16 hours of development (0-2h, 2-4h, etc.), late embryos until hatching (16-30h), 3rd instar larvae and adults
Project description:ChIP followed by next generation sequencing over 5 developmental time points of Drosophila virilis embryos (w[-], white eye mutation line) against 5 key mesodermal factors (Twist, Tinman, Mef2, Bagpipe and Biniou) were performed. The aim was to compare binding profiles of these 5 mesodermal factors between two Drosophila species, D. melanogaster (Zinzen et al., 2009) and D. virilis (this study). D. virilis specific antibodies were used for this purpose for 4 of the 5 factors (D. melanogaster Anti-body for Mef2 showed high specificity in D. virilis). Two biological replicates for each condition were sequenced using Illumina HiSeq.
Project description:Gene annoation and determination of gene expression levels in Drosophila virilis and Drosophila yakuba by deep sequencing. Total RNA-seq data from heads of 2-5 day old mated D virilis and D yakuba females, 1 sample from each species.
Project description:DNase-seq over 3 matching developmental time points in Drosophila melanogaster and Drosophila virilis embryos was performed. The aim is to assess conservation of hypersensitive regions between two distantly related species. Samples were sequenced using Illumina HiSeq.
Project description:We utilized a candidate gene approach using custom microarray constructed for our study species Drosophila montana and D. virilis to identify genes with modulated expression patterns under low temperature conditions. The flies were exposed to four different treatments (+5°C for 6 days, 0°C for 1 hour, two periods of recovery after cold stress and a control treatment). The aim of the study was to identify potential cold-responsive genes and to investigate differences in gene expression between the species. Microarray analysis revealed altogether 31 out of 219 genes on the array to show expression changes during different stages of cold stress. Among the potential stress tolerance genes detected earlier in D. melanogaster, hsr-omega was upregulated in both species during cold acclimation, expression changes in other genes being treatment- and species specific. Our microarray study clearly showed that different stages of cold response elicit changes at least in genes involved in heat shock response, circadian rhythm and metabolism. Cold- induced gene expression was investigated comparing four different treatments to the control treatment: 1) Cold acclimation: 14 days in control conditions, then 6 days at +5°C 2) Cold hardening: 20 days in control conditions, then1 hour at 0°C 3) 15-min recovery from chill coma: the 20-day-old flies were exposed to -6°C for 16 hours, after which they were let to recover for 15 minutes 4) 1-hour recovery from chill coma: the 20-day-old flies were exposed to -6°C for 16 hours, after which they were let to recover for 1 hour. In control treatment flies were kept for 20 days at 19°C. All the flies were 20-days old at the time of sample collection, and the light:dark cycle was 22 hours of light and 2 hours of dark. Because of the limited space on the array plate, the recovery samples were collected only for D. montana. All the samples were collected 5-6 hours after the lights had been turned on in the chamber and the flies were immediately immersed in liquid nitrogen, after which they were stored at -84ºC. Three pools of ten flies were collected from each treatment group.