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Unknown,Transcriptomics,Genomics,Proteomics

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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

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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

Mus musculus

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

| PRJNA286767 | ENA

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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

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

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

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

Human Lung Adenocarcinoma Cells: control vs. mAb NJ001 treated

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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.

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