GEO DataSets

(Submitter supplied) Phenotypic evolution can result from gains and losses of genes, mutations in coding sequences, or regulatory mutations affecting gene expression. While the relative importance of these mechanisms is debated, regulatory evolution is recognized as a key driver of phenotypic diversity. In this study, we applied a phylogenetic model to discretized gene expression states (active or inactive) to investigate the evolutionary turnover of organ-specific transcriptomes, which we define as instances where gene expression is activated or deactivated in a particular organ. more...

Organism:

Drosophila yakuba; Drosophila ananassae; Drosophila eugracilis; Drosophila takahashii; Drosophila ficusphila; Drosophila kikkawai; Drosophila simulans; Drosophila elegans; Drosophila bipectinata; Drosophila biarmipes; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

33 related Platforms

176 Samples

Download data: TXT

(Submitter supplied) How evolutionary changes in genes and neurons encode species variation in complex motor behaviors are largely unknown. Here, we develop genetic tools that permit a neural circuit comparison between the model speciesDrosophila melanogasterand the closely-related speciesD. yakuba, who has undergone a lineage-specific loss of sine song, one of the two major types of male courtship song inDrosophila. Neuroanatomical comparison of song patterning neurons called TN1 across the phylogeny demonstrates a link between the loss of sine song and a reduction both in the number of TN1 neurons and the neurites serving the sine circuit connectivity. more...

Organism:

Drosophila melanogaster; Drosophila yakuba

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25244 GPL33170

2 Samples

Download data: MTX, RDS, TSV

(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 melanogaster; Drosophila pseudoobscura; Drosophila yakuba; Drosophila simulans; Drosophila suzukii; Drosophila biarmipes; Drosophila erecta; Drosophila persimilis; Drosophila ficusphila

Type:

Genome binding/occupancy profiling by high throughput sequencing

9 related Platforms

18 Samples

Download data: BW, NARROWPEAK

(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 melanogaster; Drosophila simulans; Drosophila yakuba; Drosophila suzukii; Drosophila ananassae; Drosophila subobscura; Drosophila virilis; Drosophila biarmipes

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

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

Type:

Expression profiling by high throughput sequencing

10 related Platforms

35 Samples

Download data: BW

(Submitter supplied) We use closely-related Drosophila species to understand mechanosensation and how hearing as a form of mechanosensation drives reproductive isolation and evolution. In particular, we performed RNA-seq to obtain the Johnston's Organ transcriptomes of six closely-related Drosophila species, namely, D.melanogaster, D.yakuba, D.pseudoobscura and D.persimilis. Application of the Ornstein-Uhlenbeck model identified gene expression changes between the species' auditory structures. more...

Organism:

Drosophila persimilis; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila simulans; Drosophila yakuba

Type:

Expression profiling by high throughput sequencing

5 related Platforms

5 Samples

Download data: TXT

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

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) 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 ananassae; Drosophila erecta; Drosophila miranda; Drosophila sechellia; Drosophila simulans; Drosophila virilis; Drosophila persimilis; Drosophila santomea; 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 persimilis; Homo sapiens; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila sechellia; Drosophila simulans; Drosophila yakuba; 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 ananassae; Drosophila sechellia; Drosophila simulans; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila yakuba; Drosophila persimilis; 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) 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 pseudoobscura; Drosophila grimshawi; Drosophila sechellia; Drosophila simulans; Drosophila yakuba; 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 virilis; Drosophila melanogaster; Drosophila yakuba

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23800 GPL15334 GPL23801

44 Samples

Download data: BW, TAB

(Submitter supplied) This data set contains polyA+ transcriptional profiling of sexed adult tissues/body parts and whole adults of eight Drosophila species: Drosophila melanogaster (FBsp00000001) from two strains [w1118 (FBst0005905) and Oregon-R (FBst0025211)], Drosophila yakuba (FBsp00000254), Drosophila ananassae (FBsp00000052), Drosophila pseudoobscura (FBsp00000201), Drosophila persimilis (FBsp00000188), Drosophila willistoni (FBsp00000253), Drosophila mojavensis (FBsp00000160), and Drosophila virilis (FBsp00000251). more...

Organism:

Drosophila melanogaster; Drosophila pseudoobscura; Drosophila ananassae; Drosophila persimilis; Drosophila yakuba; synthetic construct; Drosophila mojavensis; Drosophila virilis; Drosophila willistoni

Type:

Expression profiling by high throughput sequencing

12 related Platforms

856 Samples

Download data: PDF, TXT

(Submitter supplied) The predominant form of RNA editing in animals is the enzymatic conversion of adenosine to inosine that is sequenced in cDNA as guanine. While RNA editing should be identifiable from RNA-seq data alone, genomic SNPs as well as sequencing and mapping errors result in a high false-positive rate. We used Inosine Chemical Erasing (ICE) with deep sequencing (ICE-seq) in order to validate A-to-I RNA editing genome-wide without the need for the sequencing of the underlying genomic DNA. more...

Organism:

Drosophila melanogaster; Drosophila yakuba

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19132 GPL19131 GPL17275

20 Samples

Download data: BED, TXT

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

Organism:

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

Type:

Expression profiling by high throughput sequencing; Other

10 related Platforms

66 Samples

Download data: TXT

(Submitter supplied) We applied microfluidic multiplex PCR and deep sequencing (mmPCR-seq) and targeted RNA sequencing to quantify RNA editing levels at targeted sites in 6 Drosophila species and 8 strains of D. melanogaster.

Organism:

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

Type:

Expression profiling by high throughput sequencing; Other

9 related Platforms

52 Samples

Download data: TXT

(Submitter supplied) In gonadal tissues, the Piwi-interacting (piRNA) pathway preserves genomic integrity by employing 23-29nt small RNAs complexed with argonaute proteins to suppress parasitic mobile sequences of DNA called transposable elements (TEs). While recent evidence suggests that the piRNA pathway may be present in select somatic cells outside the gonads, the role of a non-gonadal somatic piRNA pathway is not well characterized. more...

Organism:

Drosophila melanogaster; Drosophila yakuba; Drosophila simulans

Type:

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

Platforms:

GPL22293 GPL17275 GPL22610

24 Samples

Download data: TXT