GEO DataSets

(Submitter supplied) Both cis- and trans-acting changes could accumulate and participate in complex interactions, so to isolate the cis-regulatory component of patterning evolution, we measured allele-specific spatial gene expression patterns in Drosophila melanogaster × D. simulans hybrid embryos. RNA-seq of cryosectioned slices revealed 55 genes with strong spatially-varying allele-specific expression, and several hundred more with weaker but significant spatial divergence. more...

Organism:

Drosophila melanogaster; Drosophila simulans; Drosophila melanogaster x Drosophila simulans

Type:

Expression profiling by high throughput sequencing

4 related Platforms

186 Samples

Download data: TSV, TXT

(Submitter supplied) Species-specific regulation of gene expression contributes to the development and maintenance of reproductive isolation and to species differences in ecologically important traits. A better understanding of the evolutionary forces which shape regulatory variation and divergence can be developed by comparing expression differences among species and interspecific hybrids. Once expression differences are identified, the underlying genetics of regulatory variation or divergence can be explored. more...

Organism:

Drosophila simulans; Drosophila melanogaster; Drosophila sp. (in: flies)

Type:

Expression profiling by genome tiling array

Platform:

GPL5919

24 Samples

Download data: BAR, CEL

(Submitter supplied) Analysis of differential expression using the 3’ expression module revealed 34% probe sets showed evidence for a sex bias and alternative exon sex bias was identified for 164 genes. Intriguingly, allelic imbalance was detected for 37% of 6,579 probe sets examined which contained heterozygous SNP loci.

Organism:

Drosophila simulans

Type:

Expression profiling by array; Other

Platform:

GPL11273

15 Samples

Download data: CEL, CSV

(Submitter supplied) RNA was extracted from adult male and adult female Drosophila simulans carrying small genomic segments introgressed from Drosophila mauritiana

Organism:

Drosophila melanogaster; Drosophila simulans; Drosophila mauritiana

Type:

Expression profiling by array

Platform:

GPL6056

64 Samples

Download data: GPR, TXT

(Submitter supplied) The X chromosome has a large effect on hybrid dysfunction, particularly hybrid male sterility. Although the evidence for this so-called large-X effect is clear, its molecular causes are not yet fully understood. One possibility is that, under certain conditions, evolution proceeds faster in X-linked loci than in their autosomal counterparts due to both natural selection and their hemizygosity in males (i.e. more...

Organism:

Drosophila santomea; Drosophila yakuba; Drosophila yakuba x Drosophila santomea

Type:

Expression profiling by array

Platform:

GPL15708

18 Samples

Download data: TXT

(Submitter supplied) Using RNA-seq technology, a comprehensive assessment of cis regulatory divergence in interspecific hybrid female heads was conducted and patterns of sequence evolution (Begun et al. 2007) within causal loci were examined. Genotype specific references were shown to virtually eliminate the map bias plaguing this technology. A novel Bayesian model, which uses allele representation in F1 hybrid DNA sequence reads as a prior, was used to estimate allele frequencies in RNA sequences.

Organism:

Drosophila melanogaster x Drosophila simulans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15045

3 Samples

Download data: CSV

(Submitter supplied) These data were generated in a study to analyze the genetic causes of gene regulatory divergence. mRNA-seq libraies were prepared from poly(A)+ RNA prepared from whole F1 hybrids of D. melanogaster and D. sechellia (female 0-3d post eclosion, "D_mel_x_D_sec"). A mixed mRNA- seq library was prepared from D. melanogaster and D. sechellia poly(A) + RNA (mixed before library preparation, "D_mel_+_D_sec). more...

Organism:

Drosophila melanogaster; Drosophila sechellia; Drosophila melanogaster x Drosophila sechellia

Type:

Expression profiling by high throughput sequencing

4 related Platforms

4 Samples

Download data: BED

(Submitter supplied) Transcription is controlled by the interactions of cis-acting DNA elements with diffusible trans-acting factors. Changes in cis or trans factors can drive expression divergence within and between species, and the relative prevalence of each can reveal the evolutionary path to variation. Previous work delineating the mode of expression divergence in animals has largely used whole body expression measurements in a single condition. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

48 Samples

Download data: TXT

(Submitter supplied) Young, or newly evolved, genes arise ubiquitously across the tree of life, and can rapidly acquire novel functions that influence a diverse array of biological processes (Chen et al. 2013)1. Previous work identified a young regulatory gene in Drosophila, Zeus, which diverged rapidly from its parent Caf40 and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the Drosophila melanogaster genome Chen et al. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

13 Samples

Download data: BED

(Submitter supplied) This experiment was designed to study the transcriptional alternations using RNA-seq technique. RNA materials were collected and sequenced with multiple experimental groups in tri-plicates as follows: control-knockout-replicate 1~3 (KO-Ctrl__1~3), Zeus-knockout-replicate 1~3 (KO-Zeus__1~3), for RNA-sequencing. In total, 6 sequencing files were downloaded from the genomic core facility, University of Chicago. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21306

6 Samples

Download data: TXT

(Submitter supplied) Both cis and trans regulatory evolution underlies phenotypic innovation and diversification. However, how the nascent trans regulators escape negative pleiotropy, which may constrain their evolution and contribution to adaptation, remain unclear. Here, we compare the testis transcriptomes at single-cyst level between knockout lines of miRNA-983, an adaptively evolving young miRNA, in D. melanogaster and D. more...

Organism:

Drosophila melanogaster; Drosophila simulans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23702 GPL31091

122 Samples

Download data: TXT

(Submitter supplied) We sequenced mRNA from transverse slices of embryos at the blastoderm stage to determine genome-wide patterns of gene expression.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

122 Samples

Download data: CUFF, 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 melanogaster; Drosophila pseudoobscura; Drosophila yakuba; 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) This is a dataset which comprises the following two different kinds of genomic data in Drosophila species: First, triplicate ChIP-seq data of CTCF (CCCTC binding factor) binding profiles in each of the four closely related Drosophila species : Drosophila melanogaster, Drosophila simulans, Drosophila yakuba and Drosophila pseudoobscura at white pre pupa stage; Second, triplicate RNA-seq data of white pre pupa whole animals of three Drosophila species: Drosophila melanogaster, Drosophila simulans and Drosophila yakub. more...

Organism:

Drosophila melanogaster; Drosophila yakuba; Drosophila simulans; Drosophila pseudoobscura

Type:

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

4 related Platforms

21 Samples

Download data: BED, TXT, WIG