GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila mojavensis; Drosophila persimilis; Drosophila azteca; Drosophila takahashii; Drosophila erecta; Drosophila pseudoobscura; Drosophila ficusphila; Drosophila ananassae; Drosophila subobscura; Drosophila virilis; Drosophila biarmipes; Drosophila melanogaster; Drosophila simulans; Drosophila yakuba; Drosophila suzukii

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

20 related Platforms

118 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) The PIWI-interacting RNA (piRNA) pathway plays a crucial role in preventing endogenous genomic parasites, transposable elements (TEs), from damaging the genetic material of animal gonadal cells. Specific regions in the genome, called piRNA clusters, define each species’ piRNA repertoire and therefore its capacity to recognize and silence transposons. In the somatic cells of the Drosophila melanogaster ovary, the flamenco (flam) unistrand cluster is the main source of piRNAs and primarily regulates Gypsy family TEs that are able to form virus-like particles and infect neighbouring germ cells. more...

Organism:

Drosophila persimilis; Drosophila takahashii; Drosophila bifasciata; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila subobscura; Drosophila ficusphila; Drosophila simulans; Drosophila yakuba; Drosophila suzukii; Drosophila ananassae; Drosophila erecta; Drosophila mojavensis; Drosophila virilis; Drosophila azteca; Drosophila biarmipes

Type:

Non-coding RNA profiling by high throughput sequencing

15 related Platforms

65 Samples

Download data: BW

(Submitter supplied) The PIWI-interacting RNA (piRNA) pathway plays a crucial role in preventing endogenous genomic parasites, transposable elements (TEs), from damaging the genetic material of animal gonadal cells. Specific regions in the genome, called piRNA clusters, define each species’ piRNA repertoire and therefore its capacity to recognize and silence transposons. In the somatic cells of the Drosophila melanogaster ovary, the flamenco (flam) unistrand cluster is the main source of piRNAs and primarily regulates Gypsy family TEs that are able to form virus-like particles and infect neighbouring germ cells. more...

Organism:

Drosophila ananassae; Drosophila persimilis; Drosophila takahashii; Drosophila bifasciata; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila subobscura; Drosophila ficusphila; Drosophila erecta; Drosophila mojavensis; Drosophila virilis; Drosophila azteca; Drosophila biarmipes; Drosophila simulans; Drosophila yakuba; Drosophila suzukii

Type:

Expression profiling by high throughput sequencing

10 related Platforms

35 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster; Drosophila virilis

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL21306 GPL25244 GPL32718

34 Samples

Download data: BED, CSV, H5, MCOOL, TSV

(Submitter supplied) Here we present evidence for a new level of genome folding, whereby distant domains megabases apart fuse to form meta-domains. Within meta-domains, certain gene promoters pair with structural intergenic elements in the distant TAD. These long-range associations occur in a large fraction of Drosophila neurons, but support transcription in only a subset of cells in the nervous system. Most of the associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. more...

Organism:

Drosophila virilis; Drosophila melanogaster

Type:

Other

Platforms:

GPL32718 GPL25244

30 Samples

Download data: MCOOL

(Submitter supplied) The dosage compensation complex (DCC) of Drosophila identifies its X chromosomal binding sites with exquisite selectivity. The principles that assure this vital targeting are known from the D. melanogaster model: DCC-intrinsic specificity of DNA binding, cooperativity with the CLAMP protein, and non-coding roX2 RNA transcribed from the X chromosome. We found that in D. virilis, a species separated from melanogaster by 40 million years of evolution, all principles are active, but contribute differently to X-specificity. more...

Organism:

Drosophila melanogaster; Drosophila virilis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19951 GPL29678

73 Samples

Download data: BW

(Submitter supplied) Expression profiling by high-throughput sequencing (RNA-seq) across eight WT Drosophila species - D. melanogaster, D. simulans, D. yakuba, D. ananassae, D. pseudoobscura, D. willistoni, D. mojavensis and D. virilis - and three tissues, namely, brain, eye-antennal and imaginal discs, at the stage of third instar larvae.

Organism:

Drosophila simulans; Drosophila yakuba; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila ananassae; Drosophila mojavensis; Drosophila virilis; Drosophila willistoni

Type:

Expression profiling by high throughput sequencing

8 related Platforms

27 Samples

Download data: TXT

(Submitter supplied) Total RNA seq from different species fly heads at different temperatures

Organism:

Drosophila simulans; Drosophila yakuba; Drosophila virilis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19131 GPL23865 GPL20240

18 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila virilis; Drosophila melanogaster; Drosophila simulans; Drosophila yakuba

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Expression profiling by array

5 related Platforms

104 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster; Drosophila virilis; Drosophila busckii

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

4 related Platforms

17 Samples

Download data: BED, BW, H5

(Submitter supplied) We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. more...

Organism:

Drosophila virilis; Drosophila busckii; Drosophila melanogaster

Type:

Other; Third-party reanalysis

4 related Platforms

5 Samples

Download data: BED, FA, GTF, H5, TXT

(Submitter supplied) We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. more...

Organism:

Drosophila busckii; Drosophila virilis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25633 GPL25632

12 Samples

Download data: BW

(Submitter supplied) The earliest stage of animal development is controlled by maternally deposited mRNA transcripts and proteins. Once the zygote is able to transcribe its own genome, maternal transcripts are degraded, in a tightly regulated process known as the maternal to zygotic transition (MZT). While this process has been well-studied within model species, we have little knowledge of how the pools of maternal and zygotic transcripts evolve. more...

Organism:

Drosophila ananassae; Drosophila erecta; Drosophila miranda; Drosophila sechellia; Drosophila simulans; Drosophila virilis; Drosophila persimilis; Drosophila santomea; Drosophila melanogaster; Drosophila yakuba; Drosophila mauritiana; Drosophila mojavensis; Drosophila pseudoobscura; Drosophila willistoni

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

14 related Platforms

119 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster; Drosophila pseudoobscura; Drosophila sechellia; Drosophila simulans; Drosophila yakuba; Drosophila persimilis; Homo sapiens; Drosophila ananassae; Drosophila erecta; Drosophila mojavensis; Drosophila virilis; Drosophila willistoni

Type:

Genome binding/occupancy profiling by high throughput sequencing

15 related Platforms

175 Samples

Download data: BW

(Submitter supplied) Transcriptional enhancers function as docking platforms for combinations of transcription factors to control gene expression. How enhancer sequences determine nucleosome occupancy, transcription factor recruitment, and transcriptional activation in vivo remains unclear. Using ATAC-seq across a panel of Drosophila inbred strains we found that SNPs affecting Grainyhead binding sites causally determine the accessibility of epithelial enhancers. more...

Organism:

Drosophila melanogaster; Drosophila pseudoobscura; Drosophila yakuba; Drosophila persimilis; Drosophila ananassae; Drosophila sechellia; Drosophila simulans; Drosophila erecta; Drosophila mojavensis; Drosophila virilis; Drosophila willistoni

Type:

Genome binding/occupancy profiling by high throughput sequencing

12 related Platforms

24 Samples

Download data: BW

(Submitter supplied) Syndromes of hybrid dysgenesis (HD) have been critical for our understanding of the transgenerational maintenance of genome stability by piRNA. HD in D. virilis represents a special case of HD since it includes simultaneous mobilization of a set of TEs that belong to different classes. The standard explanation for HD is that eggs of the responder strains lack an abundant pool of piRNAs corresponding to the asymmetric TE families transmitted solely by sperm. more...

Organism:

Drosophila virilis

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL20240 GPL15873

19 Samples

Download data: XLSX

(Submitter supplied) We overexpressed the conspecific miR-975 in the cell lines derived from multiple Drosophila species (i.e. S2 cells from Drosophila melanogaster; ML82-19a cells from Drosophila simulans and WR-Dv-1 cells from Drosophila virilis). Comparison of the miR-975 effect between different cell lines provide insight into the rewiring of regulatory network through the evolution of new microRNA.

Organism:

Drosophila virilis; Drosophila melanogaster; Drosophila simulans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13306 GPL13304 GPL13313

12 Samples

Download data: TXT

(Submitter supplied) Annotation of small RNAs from 11 Drosophila species for the purpose of non-coding RNA annotation and comparative genomics assessment.

Organism:

Drosophila grimshawi; Drosophila sechellia; Drosophila simulans; Drosophila yakuba; Drosophila mojavensis; Drosophila persimilis; Drosophila willistoni; Drosophila pseudoobscura; Drosophila ananassae; Drosophila erecta; Drosophila virilis

Type:

Non-coding RNA profiling by high throughput sequencing

22 related Platforms

56 Samples

Download data: TXT

(Submitter supplied) we generated developmental and tissue-specific 3'-seq libraries from D. yakuba and D. virilis to study the role of alternative polyadenylation across Drosophila species

Organism:

Drosophila melanogaster; Drosophila yakuba; Drosophila virilis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23800 GPL15334 GPL23801

44 Samples

Download data: BW, TAB

(Submitter supplied) By the onset of morphogenesis, Drosophila embryos consist of about 6000 cells that express distinct gene combinations. Here, we used single-cell sequencing of precisely staged embryos and devised DistMap, a computational mapping strategy to reconstruct the embryo and to predict spatial gene expression approaching single-cell resolution. We produce a virtual embryo with about 8000 expressed genes per cell. more...

Organism:

Drosophila melanogaster; Drosophila virilis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19132 GPL20240 GPL23079

9 Samples

Download data: TXT