GEO DataSets

(Submitter supplied) We used DamID-seq to analyze the genome-wide binding patterns of the group B Sox proteins Dichaete and SoxNeuro in four species of Drosophila: D. melanogaster, D. simulans, D. yakuba and D. pseudoobscura. Both binding site turnover between species and a comparison of the binding properties of the two partially-redundant transcription factors were analyzed. We found that, despite widespread turnover, genomic intervals that are commonly bound by both Dichaete and SoxNeuro are highly conserved in Drosophila.

Organism:

Drosophila simulans; Drosophila yakuba; Drosophila melanogaster; Drosophila pseudoobscura

Type:

Genome binding/occupancy profiling by high throughput sequencing

5 related Platforms

30 Samples

Download data: BED, BEDGRAPH

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

Organism:

Drosophila melanogaster

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL14121 GPL15641

47 Samples

Download data: PAIR, SGR, TXT

(Submitter supplied) Genome-wide binding of SoxN in wild type embryos: SoxNDam (DamID, stage 8-11), SoxND1 (ChIP, stage 8-11), SoxND2 (ChIP, stage 8-11), SoxNPA179 Early (ChIP, stage 7-10), and SoxNPA179 Late (ChIP, stage 11-13).

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15641

15 Samples

Download data: PAIR, SGR

(Submitter supplied) Genome-wide binding of transcription factors SoxN and D in stage 12-17 wild type embryos (SoxNDam and DDam), of SoxN in D mutants (D-SoxNDam) and of D in SoxN mutants (SoxN-DDam).

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15641

12 Samples

Download data: PAIR, SGR

(Submitter supplied) Timecourse of gene expression changes in Drosophila SoxN homozygous mutant embryos compared with their heterozygous siblings, from stage 7 to 13 of embryonic development.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL14121

20 Samples

Download data: TXT

(Submitter supplied) Whole-chromatin profile (FAIRE-seq) in three Drosophila species (D. melanogaster, D. pseudoobscura and D. virilis) in eye-antennal imaginal discs at the stage of third instar wandering larvae.

Organism:

Drosophila virilis; Drosophila melanogaster; Drosophila pseudoobscura

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13313 GPL13304 GPL13310

4 Samples

Download data: BW, 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 pseudoobscura; Drosophila simulans; Drosophila melanogaster; Drosophila yakuba

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

(Submitter supplied) We performed ChIP-chip analysis using sheared chromatin isolated from Drosophila embryos of 1-3 hours in age. Keywords: high-resolution tiling array, drosophila, twist, dorsal, snail, weckle

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL7286 GPL7285 GPL7287

15 Samples

Download data: PAIR

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

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) [original title] Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. We demonstrate extensive quantitative changes in binding of six factors that control early embryonic patterning between two closely related Drosophila species

Organism:

Drosophila melanogaster; Drosophila yakuba

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9061 GPL10061

20 Samples

Download data: GFF, TXT

(Submitter supplied) Insulators are considered as chromosome organizers. BEAF, one of the insulator proteins, is highly conserved in Drosophila speies but also limited to Drosophila spcies. BEAF associates with TSS of active genes. Comparative study of BEAF binding landscapes in four Drosophila species reveals BEAF association with gene pairs, and the results suggest the role of gain or loss of BEAF binding during the speciation of Drosophila species.

Organism:

Drosophila simulans; Drosophila virilis; Drosophila melanogaster; Drosophila pseudoobscura

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

8 Samples

Download data: BED