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Items: 1 to 20 of 485

1.

Temporal dynamics of gene expression during metamorphosis in two distant Drosophila species

(Submitter supplied) Complete metamorphosis of holometabolous insects is a complex biological process characterized by profound morphological, physiological, and transcriptional changes. To reveal the temporal dynamics of gene expression during this critical developmental transition, a detailed analysis of the developmental transcriptomes of two Drosophila species, Drosophila melanogaster and Drosophila virilis, was conducted. more...
Organism:
Drosophila melanogaster; Drosophila virilis
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL34604 GPL21306
60 Samples
Download data: CSV
Series
Accession:
GSE269951
ID:
200269951
2.

Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Drosophila erecta; Drosophila pseudoobscura; Drosophila ficusphila; Drosophila mojavensis; Drosophila persimilis; Drosophila azteca; Drosophila takahashii; 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
Series
Accession:
GSE225889
ID:
200225889
3.

Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus [small RNA-Seq]

(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 bifasciata; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila subobscura; Drosophila ficusphila; Drosophila persimilis; Drosophila takahashii; 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
Series
Accession:
GSE225888
ID:
200225888
4.

Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus [RNA-Seq]

(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 bifasciata; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila subobscura; Drosophila ficusphila; Drosophila ananassae; Drosophila persimilis; Drosophila takahashii; 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
Series
Accession:
GSE225887
ID:
200225887
5.

Chromosome-level organization of the regulatory genome in the Drosophila nervous system

(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 GPL32718 GPL25244
34 Samples
Download data: BED, CSV, H5, MCOOL, TSV
Series
Accession:
GSE214707
ID:
200214707
6.

Chromosome-level organization of the regulatory genome in the Drosophila nervous system [Hi-C]

(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 melanogaster; Drosophila virilis
Type:
Other
Platforms:
GPL25244 GPL32718
30 Samples
Download data: MCOOL
Series
Accession:
GSE214704
ID:
200214704
7.

Diverging principles of selective sex chromosome regulation during evolution of Drosophila

(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:
GPL29678 GPL19951
73 Samples
Download data: BW
Series
Accession:
GSE165833
ID:
200165833
8.

Evolutionary changes in cis regulation are associated with altered chromatin activity and gene expression levels in the Drosophila eye development (RNA-Seq)

(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 ananassae; Drosophila mojavensis; Drosophila virilis; Drosophila willistoni; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila simulans; Drosophila yakuba
Type:
Expression profiling by high throughput sequencing
8 related Platforms
27 Samples
Download data: TXT
Series
Accession:
GSE59707
ID:
200059707
9.

Total RNA from different species fly heads

(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 GPL20240 GPL23865
18 Samples
Download data: TXT
Series
Accession:
GSE124142
ID:
200124142
10.

Differences in circadian rhythms in fly at different temperatures

(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
Series
Accession:
GSE124136
ID:
200124136
11.

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Drosophila virilis; Drosophila busckii; Drosophila melanogaster
Type:
Genome binding/occupancy profiling by high throughput sequencing; Other
4 related Platforms
17 Samples
Download data: BED, BW, H5
Series
Accession:
GSE120752
ID:
200120752
12.

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [HiC]

(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; Drosophila melanogaster
Type:
Other; Third-party reanalysis
4 related Platforms
5 Samples
Download data: BED, FA, GTF, H5, TXT
Series
Accession:
GSE120751
ID:
200120751
13.

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [ChIP-seq]

(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
Series
Accession:
GSE120750
ID:
200120750
14.

Evolution of maternal and zygotic mRNA complements in the early Drosophila embryo

(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 melanogaster; Drosophila yakuba; Drosophila persimilis; Drosophila santomea; Drosophila ananassae; Drosophila erecta; Drosophila miranda; Drosophila sechellia; Drosophila simulans; Drosophila virilis; 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
Series
Accession:
GSE112858
ID:
200112858
15.

The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Drosophila persimilis; Homo sapiens; Drosophila sechellia; Drosophila simulans; Drosophila yakuba; Drosophila melanogaster; Drosophila pseudoobscura; 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
Series
Accession:
GSE102441
ID:
200102441
16.

The transcription factor Grainyhead primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes [evolutionary study]

(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 ananassae; Drosophila sechellia; Drosophila simulans; Drosophila persimilis; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila yakuba; 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
Series
Accession:
GSE102439
ID:
200102439
17.

Stochastic gain of susceptibility suggests a novel mechanism of resistance to hybrid dysgenesis in Drosophila virilis

(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
Series
Accession:
GSE108298
ID:
200108298
18.

miR-975 overexpression effect on Drosophila cell lines

(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:
GPL13304 GPL13306 GPL13313
12 Samples
Download data: TXT
Series
Accession:
GSE107390
ID:
200107390
19.

Small RNAs from 11 Drosophila species

(Submitter supplied) Annotation of small RNAs from 11 Drosophila species for the purpose of non-coding RNA annotation and comparative genomics assessment.
Organism:
Drosophila mojavensis; Drosophila persimilis; Drosophila willistoni; Drosophila grimshawi; Drosophila sechellia; Drosophila simulans; Drosophila yakuba; 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
Series
Accession:
GSE98013
ID:
200098013
20.

Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species

(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 virilis; Drosophila melanogaster; Drosophila yakuba
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL15334 GPL23801 GPL23800
44 Samples
Download data: BW, TAB
Series
Accession:
GSE101603
ID:
200101603
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