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Project description:The goals of this study are to perform quantitative comparison of whole transcriptome of Drosophila melanogaster 1st instar larvae central neural system (L1CNS) from three genotypes: Canton-S, elav5 single mutant, and elav5/fne double mutant; and the global 3'-end features of Drosophila melanogaster 1st instar larvae central neural system from three genotypes: Canton-S, elav5 single mutant. Total RNAs were extracted from dissected L1CNS of Drosophila melanogaster Canton-S, elav5 single mutant, and elav5/fne double mutant; total RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Prep kit with replicates for each genotype; final cDNA libraries were sequenced on Illumina HiSeq-1000 sequencer with PE-100 mode. Total RNA-seq data were mapped to the corresponding UCSC genome assemblies: Drosophila melanogaster (dm6), HISAT2 aligner was used for the alignment with default parameters. We found that L1CNS from Canton-S expresses neural specific 3' UTR extensions like head, while in L1CNS from elav5 single mutant, global neural specific 3' UTR extensions are not significantly lost, but in elav5/fne double mutant L1CNS, there is a dramatic loss of neural specific 3' UTR extensions. We reported for the first time demonstration of trans-acting factors that globally maintain this very distinctive tissue-specific APA landscape.
2020-10-01 | GSE155532 | GEO
Project description:The goal of this study is to perform quantitative comparison of transcriptome-wide 3'-end features of Drosophila melanogaster 1st instar larvae central neural system (L1CNS) from three genotypes: Canton-S, elav5 single mutant, and elav5/fne double mutant; Total RNAs were extracted from dissected L1CNS of Drosophila melanogaster Canton-S, elav5 single mutant, and elav5/fne double mutant; 3'-end sequencing libraries were prepared using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit REV for Illumina with replicates for each genotype; final cDNA libraries were sequenced on Illumina HiSeq-1000 sequencer with SE-50 mode. 3'-end sequencing data were mapped onto the corresponding UCSC genome assemblies: Drosophila melanogaster (dm6) and 3′ end clusters were derived and quantified within a 25 bp window. We found that L1CNS from Canton-S expresses neural specific 3' UTR extensions like head, while in L1CNS from elav5 single mutant, global neural specific 3' UTR extensions are not significantly lost, but in elav5/fne double mutant L1CNS, there is a dramatic loss of neural specific 3' UTR extensions. We reported for the first time demonstration of trans-acting factors that globally maintain this very distinctive tissue-specific APA landscape.
2020-10-01 | GSE155531 | GEO
Project description:We have identified the protein binders of functionally distinct promoters from the Drosophila melanogaster genome using nuclear extracts prepared from Schneider S2 cells
2023-02-16 | PXD028090 | Pride
Project description:In order to characterize duplication polymorphisms in Drosophila simulans, we applied comparative genome hybridization (CGH) using tiling arrays originally designed to cover the full euchromatic genome of its sister species D. melanogaster. We only used the ~900,000 probes in the tiling arrays that had a perfect and unique match to the D. simulans genome (droSim1). We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates. The probabilities of mutation were parsed to make duplication calls. The supplementary file linked to each Sample record contains for each probe, its location in the D. simulans genome and its posterior probability of being duplicated (output from the Hiddem Markov Model)
2011-09-01 | GSE29260 | GEO
Project description:Genome assemblies of Drosophila melanogaster and Drosophila simulans natural strains from long read sequencing
| PRJEB50024 | ENA
Project description:Genome wide distribution of dH1K27me2 in Wild Type Drosophila melanogaster S2 cells
2022-08-02 | GSE167018 | GEO
Project description:The role natural selection plays in governing the locations and early evolution of copy number mutations remains largely unexplored. Here we employ high-density full-genome tiling arrays to create a fine-scale genomic map of copy number polymorphisms (CNPs) in Drosophila melanogaster. We inferred a total of 2,658 independent CNPs, 56% of which overlap genes. These include CNPs likely to be under positive selection, most notably high frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns and those falling on the X-chromosome seem to be subject to the strongest purifying selection. In order to characterize copy number polymorphisms (CNPs) in Drosophila malanogaster, we applied comparative genome hybridization (CGH) using tiling arrays covering the full euchromatic genome of Drosophila melanogaster. We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates and the reference genome strain. Training data for copy number changes were obtained via hybridization with a line known to contain a ~200kb homozygous duplication and from a set of 52 validated homozygous deletions. The probabilities of mutation were parsed to make CNP calls. Key words: comparative genomic hybridization, CGH, copy number polymorphism, CNP, copy number variation, CNV, duplication, deletion
2008-06-06 | GSE11326 | GEO
Project description:Genome wide distribution of gammaH2AvD in Wild Type and RNAi dH1 Drosophila melanogaster S2 cells
2020-07-01 | GSE76912 | GEO
Project description:Genome wide distribution of gammaH2AvD in Wild Type and RNAi dH1 Drosophila melanogaster S2 cells
2017-08-18 | GSE99004 | GEO
Project description:The basidiomycete Moniliophthora roreri causes frosty pod rot of cacao (Theobroma cacao) in the Western hemisphere. M. roreri is considered asexual and haploid throughout its hemibiotrophic lifecycle. To understand the processes driving genome modification, using long-read sequencing technology we sequenced and assembled five high quality M. roreri genomes out of a collection of ninety-nine isolates collected throughout the pathogen's range. We obtained chromosome-scale assemblies composed of eleven scaffolds. We used short-read technology to sequence the genomes of twenty-two similarly chosen isolates. Alignments among the five reference assemblies revealed inversions and segmental translocations and duplications between and within scaffolds. Isolates at the front of the pathogens’ expanding range tend to share lineage-specific structural variants, as confirmed by short-read sequencing. We identified, for the first time, three new mating type A locus alleles (five in total) and one new potential mating type B locus allele (three in total). Currently only two mating type combinations, A1B1 and A2B2, are known to exist outside of Colombia. A systematic survey of the M. roreri transcriptome across twenty-two isolates identified an expanded candidate effector pool and provided evidence that effector candidate genes unique to the Moniliophthoras have been selected for preferential expression during the biotrophic phase of disease. Notably, M. roreri isolates in Costa Rica carry a chromosome segment duplication that has doubled the associated gene complement and includes secreted proteins and candidate effectors. Clonal propagation of the haploid M. roreri genome has allowed lineages with unique genome structures and compositions to dominate as it expands its range, displaying a significant founder effect.
2023-06-01 | GSE226814 | GEO