GEO DataSets

(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

(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 mauritiana; Drosophila mojavensis; Drosophila pseudoobscura; Drosophila willistoni; Drosophila melanogaster; Drosophila yakuba; Drosophila persimilis; Drosophila santomea

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

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 erecta; Drosophila mojavensis; Drosophila virilis; Drosophila willistoni; Drosophila ananassae; Drosophila sechellia; Drosophila simulans; Drosophila persimilis

Type:

Genome binding/occupancy profiling by high throughput sequencing

12 related Platforms

24 Samples

Download data: BW

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

Organism:

Drosophila pseudoobscura; Drosophila melanogaster; Drosophila ananassae; Drosophila erecta; Drosophila simulans

Type:

Expression profiling by high throughput sequencing

5 related Platforms

119 Samples

Download data: BW

(Submitter supplied) Multicellular development is largely determined by transcriptional regulatory programs that orchestrate the expression of thousands of protein-coding and noncoding genes. To decipher the genomic regulatory code that specifies these programs, and to investigate globally the developmental relevance of noncoding transcription, we profiled genome-wide promoter activity throughout embryonic development in 5 Drosophila species. more...

Organism:

Drosophila ananassae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13309

22 Samples

Download data: BED, BW, 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 ananassae; Drosophila erecta; Drosophila virilis; Drosophila pseudoobscura; Drosophila mojavensis; Drosophila persimilis; Drosophila willistoni; Drosophila grimshawi; Drosophila sechellia; Drosophila simulans; Drosophila yakuba

Type:

Non-coding RNA profiling by high throughput sequencing

22 related Platforms

56 Samples

Download data: TXT

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

Type:

Expression profiling by high throughput sequencing

12 related Platforms

856 Samples

Download data: PDF, TXT

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

Organism:

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

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

Type:

Expression profiling by high throughput sequencing; Other

9 related Platforms

52 Samples

Download data: TXT

(Submitter supplied) Phenotypic differences between closely related species are thought to arise primarily from changes in gene expression due to mutations in cis-regulatory sequences (enhancers). However, it has remained unclear how frequently mutations alter enhancer activity or create functional enhancers de novo. Here we use STARR-seq, a recently developed quantitative enhancer assay, to determine genome-wide enhancer activity profiles for five Drosophila species in the constant trans-regulatory environment of Drosophila melanogaster S2 cells. more...

Organism:

Drosophila yakuba; Drosophila melanogaster; Drosophila pseudoobscura; Drosophila ananassae; Drosophila willistoni

Type:

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

5 related Platforms

18 Samples

Download data: TXT

(Submitter supplied) Purpose: Accurate identification of sex-biased genes requires precise measurement of gene expression levels in gonads. This study is designed to provide such data for various Drosophila species to enhance studies of sex-biased gene expression and evolution across the genus. Methods: Virgin flies were collected and aged 6-10 days before dissecting 2-3 replicates of testes or ovaries. Total RNA was extracted using the Arcturus® PicoPure® kit . more...

Organism:

Drosophila pseudoobscura; Drosophila yakuba; Drosophila ananassae

Type:

Expression profiling by high throughput sequencing

4 related Platforms

13 Samples

Download data: DIFF, TXT

(Submitter supplied) The model organism Encyclopedia of DNA Elements project (modENCODE) has produced a comprehensive annotation of D. melanogaster transcript models based on an enormous amount of high-throughput experimental data. However, some transcribed elements may not be functional, and technical artifacts may lead to erroneous inference of transcription. Inter-species comparison provides confidence to predicted annotation, since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function. more...

Organism:

Drosophila eugracilis; Drosophila takahashii; Drosophila ficusphila; Drosophila kikkawai; Drosophila bipectinata; Drosophila rhopaloa; Drosophila ananassae; Drosophila simulans; Drosophila virilis; Drosophila elegans; Drosophila biarmipes; Drosophila mojavensis; Drosophila yakuba; Drosophila melanogaster; Drosophila pseudoobscura

Type:

Expression profiling by high throughput sequencing

34 related Platforms

93 Samples

Download data: BAM, BED, RPKM, TXT

(Submitter supplied) We sequenced mRNA from whole flies of females and male of Drosophila melanogaster, D. simulans, D. yakuba, D. ananassae, D. pseudobscura, D. mojavensis, and D. virilis as part of the modENCODE project to validate novel gene models found in D. melanogaster, identify genes differentially expressed between the sexes and sex-specific alternative splicing events, and examine the evolution of gene expression.

Organism:

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

Type:

Expression profiling by high throughput sequencing

14 related Platforms

32 Samples

Download data: BAM, RPKM, TXT