GEO DataSets

(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) The earliest stages of development in most metazoans are driven by maternally deposited proteins and mRNAs, with widespread transcriptional activation of the zygotic genome occurring hours after fertilization, at a period known as the maternal-to-zygotic transition (MZT). In Drosophila, the MZT is preceded by the transcription of a small number of genes that initiate sex determination, patterning and other essential developmental processes. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11203

3 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) In all animals, the initial events of embryogenesis are controlled by maternal gene products that are deposited into the developing oocyte. At some point after fertilization, control of embryogenesis is transferred to the zygotic genome in a process called the maternal to zygotic transition (MZT). During this time maternal RNAs are degraded and zygotic RNAs are transcribed1. A long standing question has been, what factors regulate these events? The recent findings that microRNAs and Smaugs mediate maternal transcript degradation brought new life to this old problem2,3, however, the transcription factors that activate zygotic gene expression remained elusive. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Dataset:

GDS3477

Platform:

GPL1322

6 Samples

Download data: CEL

Analysis of embryos lacking the zinc finger protein Zelda. Results provide insight into the role of Zelda in the transfer of control of embryogenesis to the zygotic genome during the process of maternal-to-zygotic transition.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL1322

Series:

GSE11231

6 Samples

Download data: CEL

(Submitter supplied) We used FAIRE-seq to perform genome-wide profiling of open chromatin in 2-3 hour Drosophila embryos lacking maternal ZLD (zldM-) and in paired control embryos (yw). We demonstrate that ZLD is required to establish or maintain specific regions of open chromatin. Using single embryo RNA-seq data (from stage 5 yw and zldM- embryos) we show that loci that lose accessibility in zldM- embryos require ZLD for robust expression of associated genes. more...

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL13304

6 Samples

Download data: BIGWIG, TXT

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

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL21306 GPL19132 GPL25244

50 Samples

Download data

(Submitter supplied) Following fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are essential for remodeling the chromatin and driving the initial wave of zygotic gene expression. In Drosophila melanogaster, the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal- to-zygotic transition (MZT). more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

6 Samples

Download data: TXT

(Submitter supplied) Following fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are essential for remodeling the chromatin and driving the initial wave of zygotic gene expression. In Drosophila melanogaster, the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal-to-zygotic transition (MZT). more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

12 Samples

Download data: BED, BW

(Submitter supplied) Following fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are essential for remodeling the chromatin and driving the initial wave of zygotic gene expression. In Drosophila melanogaster, the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal-to-zygotic transition (MZT). more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21306

32 Samples

Download data: BED, BW

(Submitter supplied) A conspicuous feature of early animal development is the lack of transcription from the embryonic genome, and it typically takes several hours to several days (depending on the species) until widespread transcription of the embryonic genome begins. Although this transition is ubiquitous, relatively little is known about how the shift from a transcriptionally quiescent to transcriptionally active genome is controlled. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

50 Samples

Download data: WIG, XLS

(Submitter supplied) A central question in biology is how enhancers are made accessible. The Drosophila embryo is a good model system to study this question as the gene regulatory networks regulating early developmental events have been well characterized. Zelda (Zld) is a uniformly distributed transcription factor (TF) integral to these networks, acting prior to and in collaboration with the patterning TFs to regulate target enhancers. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL11203 GPL13304 GPL17275

32 Samples

Download data: BW, TXT

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

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL9058 GPL1322

10 Samples

Download data: BED, BEDGRAPH, CEL

(Submitter supplied) Transcription factors, which regulate the spatiotemporal patterns of gene expression during organogenesis, often regulate multiple aspects of tissue morphogenesis, including cell-type specification, cell proliferation, cell death, cell polarity, cell shape, cell arrangement and cell migration. In this work, we describe a distinct role for Ribbon (Rib) in controlling cell shape changes during elongation of the Drosophila salivary gland (SG). more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9058

4 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Transcription factors, which regulate the spatiotemporal patterns of gene expression during organogenesis, often regulate multiple aspects of tissue morphogenesis, including cell-type specification, cell proliferation, cell death, cell polarity, cell shape, cell arrangement and cell migration. In this work, we describe a distinct role for Ribbon (Rib) in controlling cell shape changes during elongation of the Drosophila salivary gland (SG). more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

6 Samples

Download data: CEL

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

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL1322

6 Samples

Download data: CEL

(Submitter supplied) Grainy head (Grh) is a conserved transcription factor (TF) controlling epithelial differentiation and regeneration. To elucidate Grh functions, we identified embryonic Grh targets by ChIP-seq and gene expression analysis. We show that Grh controls hundreds of target genes. Repression or activation correlates with the distance of Grh binding sites to the transcription start sites of its targets. Analysis of 54 Grh-responsive enhancers during development and upon wounding suggests cooperation with distinct TFs in different contexts. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9061

3 Samples

Download data: BED, FASTA

(Submitter supplied) Grainy head (Grh) is a conserved transcription factor (TF) controlling epithelial differentiation and regeneration. To elucidate Grh functions, we identified embryonic Grh targets by ChIP-seq and gene expression analysis. We show that Grh controls hundreds of target genes. Repression or activation correlates with the distance of Grh binding sites to the transcription start sites of its targets. Analysis of 54 Grh-responsive enhancers during development and upon wounding suggests cooperation with distinct TFs in different contexts. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

6 Samples

Download data: CEL

(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) As the Drosophila embryo transitions from the use of maternal RNAs to zygotic transcription, domains of “open” chromatin, with relatively low nucleosome density and specific histone marks, are established at promoters and enhancers involved in patterned embryonic transcription. However it remains unclear whether open chromatin is a product of activity - transcription at promoters and patterning transcription factor binding at enhancers - or whether it is established by independent mechanisms. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21306

7 Samples

Download data: WIG

(Submitter supplied) In nearly all metazoans, the earliest stages of development are controlled by maternally deposited mRNAs and proteins. The zygotic genome only becomes transcriptionally active hours later. Transcriptional activation is tightly coordinated with the degradation of maternally provided mRNAs during this maternal-to-zygotic transition (MZT). In Drosophila melanogaster, the transcription factor Zelda plays an essential role in widespread activation of the zygotic genome. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

6 Samples

Download data: CSV