Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

60 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Drosophila 16-20 hrs embryos: DHR3G60S/Df(2R)12 vs. w1118

ABSTRACT: Transcriptional profiling of 16-20 hrs Drosophila embryos comparing control (w1118) and DHR3 mutants (DHR3G60S/Df(2R)12) Two-condition experiment, control vs. DHR3 mutant embryos. Biological replicates: 4 replicates.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Anne-FranÃ§oise Ruaud

PROVIDER: E-GEOD-18577 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The Drosophila nuclear receptors DHR3 and betaFTZ-F1 control overlapping developmental responses in late embryos.

Ruaud Anne-Françoise AF Lam Geanette G Thummel Carl S CS

Development (Cambridge, England) 20100101 1

Studies of the onset of metamorphosis have identified an ecdysone-triggered transcriptional cascade that consists of the sequential expression of the transcription-factor-encoding genes DHR3, betaFTZ-F1, E74A and E75A. Although the regulatory interactions between these genes have been well characterized by genetic and molecular studies over the past 20 years, their developmental functions have remained more poorly understood. In addition, a transcriptional sequence similar to that observed in pr ...[more]

PMID: 20023167

Similar Datasets

Gene expression changes upon knockdown or over-expression of the ETS gene ETV4 in prostate cancer cell lines

Project description:Chromosomal abnormalities that give rise to elevated expression levels of the ETS genes ETV1, ETV4, ETV5, or ERG are prevalent in prostate cancer, but the function of these transcription factors in carcinogenesis is not clear. Previous work implicates ERG, ETV1, and ETV5 as regulators of invasive growth but not transformation in cell lines. Here we show that the PC3 prostate cancer cell line provides a model system to study the over-expression of ETV4. Anchorage independent growth assays and microarray analysis indicate that high ETV4 expression is critical for the transformation phenotype of PC3 cells. However, genes up-regulated upon ETV4 over-expression were very similar to genes up-regulated by ETV1 over-expression in the RWPE-1 normal prostate cell line. Together these data indicate that the ETV4 dependent transformation phenotype observed in PC3 cells is due to the genetic background of the cell line, rather than a distinct characteristic of ETV4. Furthermore, these findings suggest that the function of ETS genes in prostate cancer may differ based on other genetic alterations in a tumor. Two sets of two color experiments. First is PC3 cells expressing one of two independent ETV4 shRNAs versus PC3 cells expressing a control shRNA (luciferase). Second is RWPE-1 cells expressing 3xFlag tagged ETV4 versus RWPE-1 cells with a control (empty) vector.

2011-03-24 | E-GEOD-21209 | biostudies-arrayexpress

Expression profiling of DHR38-dependent transcripts in Drosophila larvae

Project description:Transcriptional profiling of Drosophila third instar larvae comparing control (w1118) and DHR38 mutants (DHR38Y214/Df(2)KetelRX32) Two-condition experiment, control vs. DHR38 mutant larvae. Biological replicates: 3 replicates.

2010-12-01 | E-GEOD-23047 | biostudies-arrayexpress

Vitamin C Promotes Positive Selection of Mouse T Cells

Project description:We discovered that vitamin C (ascorbic acid) is required for differentiation of mouse bone marrow-derived progenitor cells in T cell cultures based on OP9-DL1 stromal cells. This microarray dataset evaluates differential expression of genes in OP9-DL1 stromal cells as well as in lymphocytes developing in the cultures when a stabilized form of ascorbic acid (l-ascorbic acid 2-phosphate; pAsc) is added. Cultures were maintained in the absence of pAsc for 13 days, at which time 800 micromolar pAsc was added. Cells were harvested after 24 and 72 hours (24 hours only in the case of OP9-DL1 cells) and solubilized in Trizol. Two-condition experiment, differentiating T lymphoid cells with or without pAsc, 2 timepoints, OP9-DL1 cells with or without pAsc, 1 timepoint, no technical replicates

2011-08-23 | E-GEOD-31596 | biostudies-arrayexpress

Gene expression in Tcf4Het ApcHet mouse colon tumors compared to normal colon

Project description:The Wnt/M-NM-2-catenin pathway plays multiple/diverse roles in development by regulating gene expression via Tcf/Lef DNA binding factors. Misregulation of this pathway is thought to initiate colon adenoma formation. It is controversial whether Tcf4 (Tcf7L2) functions as an oncogene or tumor suppressor gene in colon carcinogenesis. We show here that Tcf4 haploinsufficiency results in colon tumor formation in a mouse tumor model that normally only develops small intestinal tumors. Further, we show that loss of Tcf4 early in development and in adult colon results in increased cell proliferation. These findings strongly suggest that Tcf4 normally modulates proliferation of the colonic epithelium and that disruption of Tcf4 activity increases proliferation leading to colon tumorigenesis. Taken together our in vivo studies favor a tumor suppressor function for Tcf4. 4 Normal Colon and 4 colon tumor from independent mouse tissue samples

2011-03-15 | E-GEOD-27522 | biostudies-arrayexpress

Microarray experiment to identify gene expression changes in response to Phenobarbital treatment and CncC overexpression in Drosophila.

Project description:Transcriptional profiling of mature adult w1118 males treated with phenobarbital compared to controls and heat treated HS-CncC flies compared with heat treated w1118 flies. Mature adult w1118 males were treated witheither 5% sucrose alone or 5% sucrose supplemented with 0.3% phenobarbital for six hours, following which RNA was extracted and subjected to micraoarray analysis.Similarly,mature adult w1118 flies or HS-CncC flies were subjected to heat treatment at 37oC for 30 minutes and recovered at room temperature for two hours,after which RNA was exctracted and subjected to microarray analysis.

2011-11-29 | E-GEOD-30087 | biostudies-arrayexpress

The RON receptor tyrosine kinase promotes metastasis by triggering epigenetic reprogramming through the thymine glycosylase MBD4 (gene expression array)

Project description:Metastasis is the major cause of death in cancer patients, yet the genetic/epigenetic programs that drive metastasis are poorly understood. Here, we report a novel epigenetic reprogramming pathway that is required for breast cancer metastasis. Concerted differential DNA methylation is initiated by activation of the RON receptor tyrosine kinase by its ligand, macrophage stimulating protein (MSP). Through PI3K signaling, RON/MSP promotes expression of the G:T mismatch-specific thymine glycosylase MBD4. RON/MSP and MBD4-dependent aberrant DNA methylation results in misregulation of a specific set of genes. Knockdown of MBD4 reverses methylation at these specific loci, and blocks metastasis. We also show that the MBD4 glycosylase catalytic residue is required for RON/MSP-driven metastasis. Analysis of human breast cancers revealed that this epigenetic program is significantly associated with poor clinical outcome. Furthermore, inhibition of Ron kinase activity with a new pharmacological agent blocks metastasis of patient-derived breast tumor grafts in vivo. To determine the molecular mechanisms by which RON/MSP drives breast cancer metastasis, we performed microarray gene expression profiling of MCF7, MCF7-RON/MSP and MCF7-RON/MSP-shMBD4 cells.

2014-01-02 | E-GEOD-52567 | biostudies-arrayexpress

Co-expression networks in generation of induced pluripotent stem cells

Project description:We developed an adenoviral vector, in which Yamanakaâ??s four reprogramming factors (RFs) were controlled by individual CMV promoters in a single cassette (Ad-GFP-SOcMK). This permitted coordinated expression of RFs (SOX2, OCT3/4, c-MYC and KLF4) in a cell for a transient period of time, synchronizing the reprogramming process with the majority of transduced cells assuming induced pluripotent stem cell (iPSC)-like characteristics as early as 3 days. These reprogrammed cells resembled human ES cells with regard to morphology, biomarker expression, and could be differentiated into cells of the germ layers in vitro and in vivo. These iPSC-like cells, however, failed to expand into larger iPSC colonies. The short and synchronized reprogramming process allowed us to study global transcription changes within short time intervals. Weighted Gene Co-Expression Network analysis (WGCNA) identified sixteen large gene co-expression modules, each including members of gene ontology categories involved in cell differentiation and development. In particular, the brown module contained a significant number of ES cell marker genes, whereas the turquoise module contained cell-cycle related genes that were downregulated in contrast to upregulation in human ESCs. Strong coordinated expression of all 4 RFs via adenoviral transduction may constrain stochastic processes and lead to silencing of genes important for cellular proliferation. Cells were dedifferentiated and gene expression assessed at 13 timepoints

2016-03-01 | E-GEOD-72676 | biostudies-arrayexpress

Microarray experment to identify genes differentially expressed in the DDT resistant 91R strain of Drosophila

Project description:Transcriptional profiling of mature adult 91R males compared to 91C males. RNA was extracted from mature adult 91R or 91C strain of Drosophila melanogaster and subjected to micraoarray analysis.

2014-08-31 | E-GEOD-48952 | biostudies-arrayexpress

C. elegans embryos: control vs. mes-2 mutant

Project description:Transcriptional profiling of early C. elegans embryos comparing control (N2) embryos with mes-2 mutant embryos at different developmental stages: 2E (24-40 cells), 4E (50-90 cells) and 8E stage (100-200 cells). Goal was to determine the effects of mes-2 loss on global gene expression as embryos transit from a developmentally plastic state (2E stage) to the onset of differentiation (8E stage). Our microarray data showed that early-expressed genes remain active, differentiation genes fail to reach wild-type levels in mes-2 mutant embryos at the 8E stage. Two-condition experiment, wild type vs. mes-2 embryos. Biological replicates: 3 control replicates, 3 mes-2 replicates for each stage.

2010-05-18 | E-GEOD-14913 | biostudies-arrayexpress

The polycomb repressive complex PRC2 regulates proliferation and neurogenesis in the Xenopus retina, and is governed by Wnt/beta-catenin signaling

Project description:The histone methyltransferase complex PRC2 controls key steps in developmental transitions and cell fate choices. However, its roles in vertebrate eye development remain unknown. Here we report that in Xenopus PRC2 regulates the progression of retinal progenitors from proliferation to differentiation. We show that the PRC2 core components are enriched in retinal progenitors and downregulated with differentiation. Knockdown of the PRC2 core component Ezh2 leads to reduced retinal progenitor proliferation in part due to upregulation of the cdk inhibitor p15Ink4b. In addition, while PRC2 knockdown does not alter eye patterning, retinal progenitor gene expression or expression of the neural competence factor Sox2, it does cause suppression of proneural bHLH gene expression, indicating that PRC2 is critical for the initiation of neural differentiation in the retina. Consistent with this, knocking down or blocking PRC2 function constrains the generation of most retinal neural cell types and promotes a Mueller glial cell fate decision. We also show that Wnt/?-catenin signaling acting through the receptor Frizzled 5, but independent of Sox2, regulates expression of key PRC2 subunits in the developing retina. This is consistent with a role for this pathway in coordinating proliferation and the transition to neurogenesis in the Xenopus retina. Our data establishes PRC2 as a regulator of proliferation and differentiation during eye development. Xenopus embryos were injected at the 8-cell stage with 5ng Ezh2 ATG MO or 5ng control MO (scrambled sequence of Ezh2 ATG MO) together with 400 pg mRNA for GFP as a lineage tracer. At stage 27, GFP-positive eyes were isolated by microdissection. Pools of 20-25 eyes were used to prepare total RNA for each sample on the microarray. 4 control and 4 Ezh2 ATG MO samples were hybridized to Agilent 1-color microarrays.

2013-05-30 | E-GEOD-47456 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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