Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Drosophila yakuba

SUBMITTER: Mathilde PARIS

PROVIDER: E-GEOD-50773 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 1)

Project description:We sequenced mRNA from blastoderm embryos of Drosophila melanogaster, Drosophila yakuba, Drosophila pseudoobscura and Drosophila virilis. Two samples contain pooled mRNA from several species, and the remaining 24 samples contain mRNA from a single species. Methods: Retinal mRNA profiles of Blastoderm embryos Comparison of the evolution of gene expression and regulatory TF binding in early Drosophila embryos.

2013-09-12 | E-GEOD-50766 | biostudies-arrayexpress

Binding site turnover produces pervasive quantitative changes in TF binding between closely related Drosophila species

Project description:[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 ChIP-Seq based binding measurements of six transcription factors in embryos of two Drosophila species, D.melanogaster and D.yakuba.

2010-02-18 | E-GEOD-20369 | biostudies-arrayexpress

Tissue specific Pol II Chip-Seq in the early fly embryo

Project description:In order to idetify paused promoters in vivo, we performed tissue specific Pol II Chip-seq using mutant embryos for the dorsal gradient. We used two population of cells, either dorsal ectoderm cells (gd7 embryos) or mesodermal cells (Toll10b) embryos. ChIP-seq for Pol II in various Drosophila embryos

2013-05-23 | E-GEOD-36310 | biostudies-arrayexpress

Poised RNA Polymerase II changes over developmental time and prepares genes for future expression (MNase-seq data)

Project description:Poised RNA polymerase II is predominantly found at developmental control genes and is thought to allow their rapid and synchronous induction in response to extracellular signals. How the recruitment of poised RNA Pol II is regulated during development is not known. By isolating muscle tissue from Drosophila embryos at five stages of differentiation, we show that the recruitment of poised Pol II occurs at many genes de novo and this makes them permissive for future gene expression. When compared to other tissues, these changes are stage-specific and not tissue-specific. In contrast, Polycomb group repression is tissue-specific and in combination with Pol II (the balanced state) marks genes with highly dynamic expression. This suggests that poised Pol II is temporally regulated and is held in check in a tissue-specific fashion. We compare our data to mammalian embryonic stem cells and discuss a framework for predicting developmental programs based on chromatin state. MNase-seq data for examining nucleosome occupancy in specific Drosophila tissues during development

2012-12-20 | E-GEOD-34283 | biostudies-arrayexpress

Poised RNA Polymerase II changes over developmental time and prepares genes for future expression (ChIP-seq data)

Project description:Poised RNA polymerase II is predominantly found at developmental control genes and is thought to allow their rapid and synchronous induction in response to extracellular signals. How the recruitment of poised RNA Pol II is regulated during development is not known. By isolating muscle tissue from Drosophila embryos at five stages of differentiation, we show that the recruitment of poised Pol II occurs at many genes de novo and this makes them permissive for future gene expression. When compared to other tissues, these changes are stage-specific and not tissue-specific. In contrast, Polycomb group repression is tissue-specific and in combination with Pol II (the balanced state) marks genes with highly dynamic expression. This suggests that poised Pol II is temporally regulated and is held in check in a tissue-specific fashion. We compare our data to mammalian embryonic stem cells and discuss a framework for predicting developmental programs based on chromatin state. ChIP-seq for Pol II, H3K4me3 and H3K27me3 in various Drosophila embryos and tissues

2012-12-20 | E-GEOD-34301 | biostudies-arrayexpress

Enhancer chromatin signatures predict Smad2/3 binding in Xenopus

Project description:In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic transcription and continuing through gastrulation. We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq

2014-09-17 | E-GEOD-56000 | biostudies-arrayexpress

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L (ChIP-Seq data)

Project description:TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. Building on these data, we show here that Sch9, an AGC family kinase and direct substrate of TORC1, promotes ribosome biogenesis (ribi) and ribosomal protein (RP) gene expression via direct inhibitory phosphorylation of three transcription repressors, Stb3, Dot6 and Tod6. Dephosphorylation of these factors allows them to recruit the RPD3L histone deactelyase complex to ribi/RP gene promoters. Since rRNA and tRNA transcription are also under its control, Sch9 appears to be well positioned to coordinately regulate transcriptional aspects of ribosome biogenesis. ChIP-Seq of 8 S. cerevisiae strains treated with 1NM-PP1, a small molecule inhibitor for analog-sensitive kinases such as sch9-as.

2011-07-01 | E-GEOD-29124 | biostudies-arrayexpress

HEB and E2A function as SMAD/FOXH1 cofactors

Project description:Nodal signaling, mediated through SMAD transcription factors, is necessary for pluripotency maintenance and endoderm commitment. We have identified a new motif, termed SMAD Complex Associated (SCA) that is bound by SMAD2/3/4 and FOXH1 in human embryonic stem cells (hESCs) and derived endoderm. We demonstrate that two bHLH proteins - HEB and E2A - bind the SCA motif at regions overlapping SMAD2/3 and FOXH1. Further, we show that HEB and E2A associate with SMAD2/3 and FOXH1, suggesting they form a complex at critical target regions. This association is biologically important, as E2A is critical for mesendoderm specification, gastrulation, and Nodal signal transduction in Xenopus tropicalis embryos. Taken together, E2A is a novel Nodal signaling cofactor that associates with SMAD2/3 and FOXH1 and is necessary for mesendoderm differentiation. ChIP-seq of Smad2/3 and Input in X.tropicalis, stage 10.5 embryo.

2011-08-23 | E-GEOD-30146 | biostudies-arrayexpress

Genome wide binding of Insensitive in w[1118] embryos

Project description:ChIP-seq for Drosophila Insensitive, together with IgG control. Chromatin extracted from 2.5-6h w[1118] embryos and 6.5-12h w[1118] embryos. Samples from two time points were analyzed: 2.5-6h embryos and 6.5-12h embryos. In each time point there is one Insv ChIP sample and one IgG control sample.

2013-04-04 | E-GEOD-44176 | biostudies-arrayexpress

Co-activation of GR and NF-kB leads to extensive rearrangemnet of their binding sites and target genes

Project description:Global identification of activated GR and p65 binding sites and target genes using ChIP-seq in HeLa B2 cells. generation genome-wide chromatin state-maps of GR, p65 and RNAPII in HeLa B2 cells under conditions 1) DMSO (control); 2) TA 1M-BM-5M 4hr; 3) TNFM-NM-1 10ng/ml ; 4) TA 1M-BM-5M 4hr at at third hour 10ng/ml TNF M-NM-1 was added

2011-07-01 | E-GEOD-24518 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data