Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling of E13.5 Eda null embryonic mammary buds

ABSTRACT: TNF ligand ectodysplasin-A1 contributes to embryonic mammary gland development. We searched for target genes of the Eda pathway using profiling of genes differentially expressed in Eda-null mammary buds after a short exposure to recombinant Fc-Eda-A1 protein. Microdissected E13.5 Eda-/- epithelial mammary buds from 5-6 embryos were pooled together. Other half of an embryo was used as a control and the other half as a treated sample. Littermates from 3 litters of B6CBA background were used for the analysis. Array and data analysis were performed in the Biomedicum Functional Genomics Unit (University of Helsinki, Finland).

ORGANISM(S): Mus musculus

SUBMITTER: Maria Voutilainen

PROVIDER: E-GEOD-69781 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiling of E13.5 Eda null embryonic mammary buds

Project description:TNF ligand ectodysplasin-A1 contributes to embryonic mammary gland development. We searched for target genes of the Eda pathway using profiling of genes differentially expressed in Eda-null mammary buds after a short exposure to recombinant Fc-Eda-A1 protein.

2015-11-01 | GSE69781 | GEO

Analysis of Gene Expression in PTHrP-/- Mammary Buds

Project description:Analysis of Gene Expression in PTHrP-/- Mammary Buds Supports a Role for BMP Signaling and MMP2 in the Initiation of Ductal Morphogenesis. Parathyroid hormone-related protein (PTHrP) acts on the mammary mesenchyme and is required for proper embryonic mammary development. In order to understand PTHrP’s effects on mesenchymal cells, we profiled gene expression in WT and PTHrP-/- mammary buds, and in WT and K14-PTHrP ventral skin, at E15.5. By cross-referencing the differences in gene expression between these groups, we identified 35 genes potentially regulated by PTHrP in the mammary mesenchyme, including 6 genes known to be involved in BMP signaling. One of these genes was MMP2. We demonstrated that PTHrP and BMP4 regulate MMP2 gene expression and MMP2 activity in mesenchymal cells. Using mammary bud cultures, we demonstrated that MMP2 acts downstream of PTHrP to stimulate ductal outgrowth. Future studies on the functional role of other genes on this list should expand our knowledge of how PTHrP signaling triggers the onset of ductal outgrowth from the embryonic mammary buds. Five experimental groups (WT mammary buds, PTHrP-/- mammary buds, WT ventral skin, K14WT ventral skin, K14-PTHrP ventral skin). Three replicates in each group. Differentially expressed genes are listed in the following supplementary files: GSE17654_List1a-Higher_in_KO_Buds_than_WT_Buds.txt GSE17654_List1b-Lower_in_KO_Buds_than_WT_Buds.txt GSE17654_List2a-Higher_in_WT_Skin_than_WT_Buds.txt GSE17654_List2b-Lower_in_WT_Skin_than_WT_Buds.txt

2009-08-15 | E-GEOD-17654 | biostudies-arrayexpress

Eda targets

Project description:Pools of 3 E14 eda null half skin pairs were cultured for 90 minutes or 4 hours in hanging drops of medium containing 2ug/mL of Fc-Eda-A1 (treated halves) or the equivalent amount of solvent (control halves). Biological triplicates for each condition were performed.

2011-12-24 | E-MEXP-3341 | biostudies-arrayexpress

Analysis of retinoid targets in chick embryo wing buds

Project description:Chick wing buds at Hamburger and Hamilton stage 20 were treated with DMSO, all trans retinoic acid or synthetic retinoid EC23 via ion-exchange beads implanted into the wing buds. The anterior third of treated wing buds of surviving embryos were removed 24 hours after treatment by microdissection and pooled to prepare RNA extracts for microarray analysis.

2020-12-31 | E-MTAB-2545 | biostudies-arrayexpress

Mus musculus

Project description:Gene expression profiling of E13.5 Eda null embryonic mammary buds

| PRJNA286767 | ENA

Blood vessels restrain pancreas branching, differentiation and growth

Project description:How organ size and form are controlled during development is a major question of biology. Blood vessels have been shown to be essential for early development of the liver and pancreas, and are fundamental to normal and pathological tissue growth. Here we report that non-nutritional signals from blood vessels surprisingly act to restrain pancreas growth. Elimination of endothelial cells increases the size of embryonic pancreatic buds. Conversely, VEGF-induced hypervascularization decreases pancreas size. The growth phenotype results from vascular restriction of pancreatic tip cell formation, lateral branching and differentiation of the pancreatic epithelium into endocrine and acinar cells. The effects are seen both in vivo and ex vivo, indicating a perfusion-independent mechanism. Thus the vasculature controls pancreas morphogenesis and growth by reducing branching and differentiation of primitive epithelial cells. For transcriptome analysis, RNA was isolated using QIAGEN RNeasy micro Kit from pancreatic buds of Pdx1-tTA (n=3) and littermate Pdx1-tTA; TET-VEGF (n=3) e12.5 embryos, or from e12.5 wild type pancreatic buds explanted and treated with VEGFR2i (n=5) or vehicle (n=5) for 2 days. Pooled samples were hybridized to Affymetrix mouse gene 1.0 st arrays. The arrays were RMA normalized using Partek Genomic Suite 6.5. Differentially regulated genes were selected based on p-values and ratios using t-test.

2011-09-13 | E-GEOD-32098 | biostudies-arrayexpress

MAGE-A1 Promotes Proliferation, Migration and Invasion of Human Melanoma Cells through RNA-SEQ Analysis via Affecting C-JUN-IL8-ARHGAP29 Network

Project description:To define the role of MAGE-A1 in melanoma growth and metastasis, we performed RNA-seq analysis on MAGE-A1 overexpression (OE) and knockdown (KD) models in A375 human melanoma cell line. Our results revealed that overexpression of MAGE-A1 dramatically promoted proliferation, migration, and invasion of human melanoma cells in vitro and down-regulated of MAGE-A1 inhibited tumor cell proliferation and invasion. Furthermore, MAGE-A1 exerts its tumor promoting activity via activating including ERK-MAPK signaling pathway by RNA-seq analysis. mRNA profiles of MAGE-A1 over expression (OE), knockdown (KD), pcDNA-vector control, and pRNAT-scramble control in A375 cell line were generated using Ion torrent

2016-01-04 | E-GEOD-66859 | biostudies-arrayexpress

Human Lung Adenocarcinoma Cells: control vs. mAb NJ001 treated

Project description:Transcriptional profiling of human lung adenocarcinoma cells comparing control untreated SPC-A1 cells with SPC-A1 cells treated with 300 M-BM-5g/ml mAb NJ001 for 36h Two-condition experiment, SPC-A1 vs. NJ001-SPC-A1 cells. Biological replicates: 3 control, 3 treated, independently grown and harvested. One replicate per array.

2014-08-01 | E-GEOD-59655 | biostudies-arrayexpress

Transcription profiling of limb buds from E12.5 wild type and POR conditional knock out mice

Project description:POR is the obligate electron donor for all microsomal P450 enzymes. POR was conditionally knocked out during limb development at E9.5. The experiment was set up to answer two questions. First, to investigate which genes are differentially expressed in POR deficient limb buds and are influenced by a metabolically inactive cytochrome P450 system. Second, to assess which P450 enzymes are expressed at all at E12.5 during limb development and therefore which metabolic pathways involving this group of enzymes are present at this stage. Differentially expressed genes were analysed by comparing 5 wild type control samples with 5 conditional knock out samples (whole forelimb buds each). Present calls of control samples were screened for annotated P450s to establish a list of expressed P450 enzymes at E12.5.

2008-10-31 | E-TABM-367 | biostudies-arrayexpress

FUNCTIONAL ANALYSIS OF CTCF DURING MAMMALIAN LIMB DEVELOPMENT_gene expression profiling

Project description:Limb buds were dissected from E10.75 mouse embryos and stored in RNAlater reagent (Qiagen), for genotyping. For each replicate, RNA was isolated from pools of six limb buds either of wild type or homozygous mutants, using RNeasy micro-kit (Qiagen). cRNA was synthesized according to the manufacturers instructions (Ambion) and hybridized to the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix), which interrogates ca 39,000 transcripts. Three independent RNA extractions, cDNA synthesis and array hybridizations were performed. The expression arrays data were normalized and scaled to signal intensity of 100 using GCOS 1.2 software (Affymetrix). Expression levels were analyzed using GeneSpring software (Silicon Genetics, Redwood City, CA) and Matlab 2009 (Math Works, Inc., MA). To identify differentially expressed transcripts, pair-wise comparison analysis was performed with GCOS 1.2 software (Affymetrix). A 77% cutoff in consistency of change (at least seven out of nine comparisons were either increased or decreased) was applied. Only genes that satisfied the pair-wise comparison test and displayed ?1.5 fold change in expression were considered for further analysis.

2011-11-01 | E-MEXP-2977 | 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