GEO DataSets

(Submitter supplied) Since their discovery, transposable elements have been proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, in particular by providing transcription start sites (TSSs) for host genes. To investigate their contribution to developmental gene expression, we developed RAMPAGE, a high-throughput 5'-complete cDNA sequencing approach to accurately discover TSSs, characterize their transcripts, and quantify their expression. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11203 GPL13304

36 Samples

Download data: BED, BW, TXT

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

Organism:

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

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 erecta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19321

23 Samples

Download data: BED, BW, TXT

(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 simulans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13306

22 Samples

Download data: BED, BW, TXT

(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 pseudoobscura

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13310

29 Samples

Download data: BED, BW, TXT

(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 melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

23 Samples

Download data: BED, BW, TXT

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

Organism:

Drosophila melanogaster; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10999 GPL11203 GPL13304

37 Samples

Download data: BED, BW

(Submitter supplied) 5'-complete cDNA sequencing on ribosome-depleted total RNA from the human K562 cell line. Provides high-quality, genome-wide single-base resolution profiling of transcription start sites and their expression levels.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

1 Sample

Download data: BED, BW

(Submitter supplied) RNA-Seq was used for transcriptome sequencing of 0-12 hour embryos.

Organism:

Aedes aegypti

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11087

4 Samples

Download data: BED

(Submitter supplied) To investigate how the cell-type-specific gene expression program for spermatocyte differentiation turns on in male flies, we used RNA-seq to map transcript levels, CAGE to map transcription start sites (TSS), and ATAC-seq to map chromatin accessibility as proliferating spermatogonia transition to differentiating spermatocytes. Combining these data, we showed that the promoters that turn on when germ cells become spermatocytes lack most of the canonical core promoter motifs. more...

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL19132 GPL21306

32 Samples

Download data: BED, BW, NARROWPEAK, TXT

(Submitter supplied) Transcriptional cofactors communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression, which is a hallmark of all multicellular organisms. However, the extent to which different cofactors display intrinsic specificity for distinct promoters is unclear. Testing intrinsic COF – core promoter (CP) compatibilities requires the systematic assessment of transcriptional activation for many CPs in the presence or absence of a given COF in an otherwise constant standardized reporter system. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL16791 GPL21697

22 Samples

Download data: BW, TXT

(Submitter supplied) Transcriptional cofactors communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression, which is a hallmark of all multicellular organisms. However, the extent to which different cofactors display intrinsic specificity for distinct promoters is unclear. Testing intrinsic COF – CP preferences requires the systematic assessment of transcriptional activation for many CPs in the presence or absence of a given COF in an otherwise constant standardized reporter system. more...

Organism:

Drosophila melanogaster

Type:

Other

Platforms:

GPL17275 GPL22106

134 Samples

Download data: BW, TXT

(Submitter supplied) Gene transcription in animals involves the assembly of the RNA polymerase II complex at core promoters and its cell type-specific activation by genomic enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has remained less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. more...

Organism:

Drosophila melanogaster

Type:

Other

Platforms:

GPL11203 GPL13304

39 Samples

Download data: TXT

(Submitter supplied) Genomic enhancers are important regulators of gene expression, but their identification is a challenge and methods depend on indirect measures of activity. We developed a method termed STARR-seq to directly and quantitatively assess enhancer activity for millions of candidates from arbitrary sources of DNA, enabling screens across entire genomes. When applied to the Drosophila genome, STARR-seq identifies thousands of cell type-specific enhancers across a broad continuum of strengths, linking differential gene expression to differences in enhancer activity and creating a genome-wide quantitative enhancer map. more...

Organism:

Homo sapiens; Drosophila melanogaster

Type:

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

Platforms:

GPL11154 GPL11203 GPL13304

18 Samples

Download data: TXT

(Submitter supplied) Sequencing of 5' ends of RNA molecules from control and exosome-depleted S2 cells.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

8 Samples

Download data: BED

(Submitter supplied) Promoter architecture, shape and usage play an important role in the regulation of eukaryotic gene expression. Several promoter profiling techniques have been developed to detect transcription start sites and alternative promoter usage between tissues or during development. However promoter profiling has not been utilized in studies that demand quantification of expression changes between developmental stages, tissues and conditions. more...

Organism:

Mus musculus; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23323 GPL22106 GPL16417

34 Samples

Download data: BW, TSV

(Submitter supplied) Abstract: Molecular genetic studies of Drosophila melanogaster have led to profound advances in understanding the regulation of development. Here we report gene expression patterns for nearly one-third of all Drosophila genes during a complete time course of development. Mutations that eliminate eye or germline tissue were used to further analyze tissue-specific gene expression programs. These studies define major characteristics of the transcriptional programs that underlie the life cycle, compare development in males and females, and show that large-scale gene expression data collected from whole animals can be used to identify genes expressed in particular tissues and organs or genes involved in specific biological and biochemical processes. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

4 related Platforms

170 Samples

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(Submitter supplied) Eyes absent mutant adult flies collected 0-24 hours after eclosion, with N=2 biological collections for males and females each. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL2839

4 Samples

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(Submitter supplied) Four separate biological collections of unfertilized eggs laid by wildtype females mated with sterile males, eggs dechorionated and snap-forzen in liquid nitrogen 0-1 hour after egg lay. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL2839

4 Samples

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