GEO DataSets

(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) 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:

Homo sapiens; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30203 GPL30173

13 Samples

Download data: BW

(Submitter supplied) Bulk ATAC-seq performed on whole adult brains across multiple homozigous fly lines (DGRP) in order to find caQTLs. Young adults (1-3 days) were used for all genotypes.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19132 GPL21306

44 Samples

Download data: MAT

(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; Drosophila melanogaster

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:

Homo sapiens; synthetic construct

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

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 GPL19604 GPL22106

6 Samples

Download data: BW, 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) 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:

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) We employ a massively parallel reporter assay (MPRA) to measure the ex vivo activities of hundreds of K562 and HepG2 enhancers with known transcription factor motif instances. For seven selected motifs that correspond to known or predicted activators and repressors in the two cell types, we make directed modifications of the bases corresponding to these motifs and observe the changes in enhancer activity.

Organism:

Homo sapiens; Escherichia coli

Type:

Other

Platforms:

GPL11154 GPL14548

6 Samples

Download data: TXT

(Submitter supplied) Although technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach towards understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL18573

29 Samples

Download data: TXT

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

Organism:

Drosophila melanogaster; Mus musculus; Homo sapiens

Type:

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

4 related Platforms

13 Samples

Download data: TSV

(Submitter supplied) Joint profiling of chromatin accessibility and gene expression of individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (eGRN). Here we present a new method for the inference of eGRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TF) and links these enhancers to candidate target genes. Specific TFs for each cell type or cell state are predicted based on the concordance of TF binding site accessibility, TF expression, and target gene expression. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL24247

10 Samples

Download data: TSV

(Submitter supplied) Joint profiling of chromatin accessibility and gene expression of individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (eGRN). Here we present a new method for the inference of eGRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TF) and links these enhancers to candidate target genes. Specific TFs for each cell type or cell state are predicted based on the concordance of TF binding site accessibility, TF expression, and target gene expression. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL30173

2 Samples

Download data: TSV

(Submitter supplied) Joint profiling of chromatin accessibility and gene expression of individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (eGRN). Here we present a new method for the inference of eGRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TF) and links these enhancers to candidate target genes. Specific TFs for each cell type or cell state are predicted based on the concordance of TF binding site accessibility, TF expression, and target gene expression. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

1 Sample

Download data: TSV

(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) Here, we combine comparative regulatory genomics with machine learning to investigate enhancer logic in melanoma. Through epigenomics profiling of 26 melanoma cell lines across six species, we examine the conservation of the two main melanoma states and underlying master regulators. By training a deep neural network on topic models derived from the human lines, we were able to classify not only human melanoma enhancers, but also regulatory regions in the other species. more...

Organism:

Mus musculus; Danio rerio; Equus caballus; Homo sapiens; Canis lupus familiaris; Sus scrofa domesticus

Type:

Genome binding/occupancy profiling by high throughput sequencing

7 related Platforms

23 Samples

Download data: BW

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

Organism:

Drosophila melanogaster

Type:

Other

Platforms:

GPL17275 GPL21306

34 Samples

Download data: TXT, XLS

(Submitter supplied) We generated HiC data from sorted mesodermal and non-mesodermal cells from stage 11-12 Drosophila embryos to explore the distribution of genomic contacts of silencers and non-silencers (identified elsewhere in the manuscript).

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL21306

4 Samples

Download data: TXT