GEO DataSets

(Submitter supplied) Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly understood and enhancer de novo design is considered impossible. Here we built a deep learning model, DeepSTARR, to quantitatively predict the activities of thousands of developmental and housekeeping enhancers directly from DNA sequence in Drosophila melanogaster S2 cells. more...

Organism:

synthetic construct; Homo sapiens

Type:

Other

Platforms:

GPL27609 GPL21697

4 Samples

Download data: TXT

(Submitter supplied) Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly understood and enhancer de novo design is considered impossible. Here we built a deep learning model, DeepSTARR, to quantitatively predict the activities of thousands of developmental and housekeeping enhancers directly from DNA sequence in Drosophila melanogaster S2 cells. more...

Organism:

Drosophila melanogaster; synthetic construct; Homo sapiens

Type:

Other

6 related Platforms

22 Samples

Download data: BW

(Submitter supplied) Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly understood and enhancer de novo design is considered impossible. Here we built a deep learning model, DeepSTARR, to quantitatively predict the activities of thousands of developmental and housekeeping enhancers directly from DNA sequence in Drosophila melanogaster S2 cells. more...

Organism:

Drosophila melanogaster; synthetic construct

Type:

Other

Platforms:

GPL26526 GPL25244

12 Samples

Download data: TXT

(Submitter supplied) Enhancer sequences control gene expression and comprise binding sites (motifs) for different transcription factors (TFs). Despite extensive genetic and computational studies, the relationship between DNA sequence and regulatory activity is poorly understood and enhancer de novo design is considered impossible. Here we built a deep learning model, DeepSTARR, to quantitatively predict the activities of thousands of developmental and housekeeping enhancers directly from DNA sequence in Drosophila melanogaster S2 cells. more...

Organism:

Drosophila melanogaster; synthetic construct

Type:

Other

Platforms:

GPL27609 GPL22106 GPL19604

6 Samples

Download data: BW, TXT

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

Organism:

Drosophila melanogaster; unidentified plasmid

Type:

Other

Platforms:

GPL21376 GPL19132

19 Samples

Download data: FASTA, TSV, TXT

(Submitter supplied) Activity of enhancers in Drosophila embryos was measured by highly parallel reporter assay. We examined the results of mutating binding sites for 4 poorly studied TFs individually or in combination, and characterized complex genetic interactions among the different classes of motif mutant.

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL19132

18 Samples

Download data: TXT, XLS

(Submitter supplied) Activity of enhancers in Drosophila embryos was measured by highly parallel reporter assay. We examined the results of mutating binding sites for 4 poorly studied TFs individually or in combination, and characterized complex genetic interactions among the different classes of motif mutant.

Organism:

unidentified plasmid

Type:

Other

Platform:

GPL21376

1 Sample

Download data: FASTA, TSV, TXT

(Submitter supplied) Gene expression is determined by genomic elements called enhancers, which contain short motifs bound by different transcription factors (TFs). However, how enhancer sequences and TF motifs relate to enhancer activity is unknown and general sequence requirements for enhancers or comprehensive sets of important enhancer sequence elements have remained elusive. Here, we computationally dissect thousands of functional enhancer sequences from three different Drosophila cell lines. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11203

3 Samples

Download data: TXT

(Submitter supplied) Terminal differentiation of epidermal cells in Drosophila embryos requires the activity of a transcription factor. Svb is necessary and sufficient to induce this process. pri is a regulator of Svb activity, converting it from a repressor into an activator. To characterize the downstream Svb and pri effectors in cell morphogenesis, we performed microarrays in wt, svb -/- (no gene) and pri -/- (svb repressor) mutant conditions.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

15 Samples

Download data: CEL, TXT

(Submitter supplied) Developmental programs are implemented by regulatory interactions between Transcription Factors (TFs) and their target genes, which remain yet poorly understood. While recent studies have focused on regulatory cascades of TFs that govern early development, little is known on how these are selected and controlled the ultimate cellular effectors of terminal differentiation. We addressed this question during late Drosophila embryogenesis when the finely tuned expression of a TF, Ovo/Shavenbaby (Svb), triggers the morphological differentiation of epidermal trichomes. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9058

3 Samples

Download data: BED, TXT, WIG

(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:

GPL13304 GPL11203

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:

Drosophila melanogaster; Homo sapiens

Type:

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

Platforms:

GPL11203 GPL13304 GPL11154

18 Samples

Download data: TXT

(Submitter supplied) The Drosophila transcription factor Tinman (Tin) is involved in embryonic heart development. We have analyzed genomic binding sites for Tin using a ChIP-chip strategy, making use of our high-quality antibody and Affymetrix Drosophila Tiling Arrays. We sampled to time points (early: 3-5.5h AEL and late: 5-8h AEL) that see distinct Tin expression in the embryo. Our data analysis yielded 2548 binding events in early and 988 binding events in late embryos. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5919

2 Samples

Download data: BAR, BED, CEL, SGR

(Submitter supplied) Contemporary high throughput technologies permit the rapid identification of transcription factor (TF) target genes on a genome-wide scale, yet the functional significance of TFs requires knowledge of target gene expression patterns, cooperating TFs and cis-regulatory element (CRE) structures. Here we investigated the myogenic regulatory network downstream of the Drosophila zinc finger TF Lame duck (Lmd) by combining both previously published and newly performed genomic data sets, including chromatin immunoprecipitation sequencing (ChIP-seq), genome-wide mRNA profiling, cell-specific expression patterns of putative transcriptional targets, analysis of histone mark signatures, studies of TF co-occupancy by additional mesodermal regulators, TF binding site determination using protein binding microarrays (PBMs), and machine learning of candidate CRE motif compositions. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

3 Samples

Download data: BED, WIG

(Submitter supplied) Enhancers harbor binding motifs that recruit transcription factors (TFs) for gene activation. While cooperative binding of TFs at enhancers is known to be critical for transcriptional activation of a handful of developmental enhancers, the extent TF cooperativity genome-wide is unknown. Here, we couple high-resolution nuclease footprinting with single-molecule methylation profiling to characterize TF cooperativity at active enhancers in the Drosophila genome. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

3 Samples

Download data: BW

(Submitter supplied) The goal of this study is to identify co-expressed genes downstream of Atonal and Senseless. These gene lists are used as candidate target genes (technically: as foreground sets) in computational predictions of cis-regulatory elements using the cisTargetX method (http://med.kuleuven.be/cme-mg/lng/cisTargetX). Together, the gene expression results and cis-regulatory predictions, yield a gene regulatory network underlying the early events in retinal differentiation. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

20 Samples

Download data: CEL

(Submitter supplied) Transcriptional enhancers act as docking stations for combinations of transcription factors and thereby regulate spatiotemporal activation of their target genes. A single enhancer, of a few hundred base pairs in length, can autonomously and independently of its location and orientation drive cell-type specific expression of a gene or transgene. It has been a long-standing goal in the field to decode the regulatory logic of an enhancer and to understand the details of how spatiotemporal gene expression is encoded in an enhancer sequence. more...

Organism:

Drosophila melanogaster; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30203 GPL30173

13 Samples

Download data: BW

(Submitter supplied) The Drosophila brain is a work horse in neuroscience. Single-cell transcriptome analysis, 3D morphological classification, and detailed mapping of the connectome have revealed an immense diversity of neuronal and glial cell types that underlie the wide array of functional and behavioral traits in the fruit fly. The developmental trajectories of each of these cell types, from neuroblast to mature neuron or glial cell, as well as their maintenance and plasticity in the adult brain, are controlled by gene regulatory networks (GRNs) In this study, we profiled chromatin accessibility of 240,000 single cells, spanning nine developmental time points from larval, pupal, and adult brains, and integrated this data with single-cell transcriptomes. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25244 GPL30203 GPL19132

58 Samples

Download data: BED, BW, GFF, NARROWPEAK, RDATA, RDS

(Submitter supplied) Biological systems display extraordinary robustness. Robustness of transcriptional enhancers results mainly from clusters of binding sites for the same transcription factor, and it is not clear how robust enhancers can evolve loss of expression through point mutations. Here, we report the high-resolution functional dissection of a robust enhancer of the shavenbaby gene that has contributed to morphological evolution. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

8 Samples

Download data: TXT

(Submitter supplied) In vivo crosslinking studies suggest that the Drosophila transcription factor Bicoid (Bcd) binds to several thousand sites during early embryogenesis, but it is not clear how many of these binding events are functionally important. In contrast, reporter gene studies have identified more than 60 Bcd-dependent enhancers, all of which contain clusters of the consensus binding sequence TAATCC. These studies also identified clusters of TAATCC motifs (inactive fragments) that failed to drive Bcd-dependent activation. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

8 Samples

Download data: TXT