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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse embryonic day 14 bladder, urogenital sinus, and urethra.

ABSTRACT: The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder. The central thesis is straightforward. The combination ofmicrodissected and laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here represents the gene expression profiles of the embryonic day 14 bladder, urogenital sinus, and urethra. Experiment Overall Design: Bladder, urogenital sinus, and urethra regions from embryonic day 14 SMGA/EGFP animals were microdissected and total RNA isolated for gene expression analysis using the Affymetrix MOE430 microarray chip.

ORGANISM(S): Mus musculus

SUBMITTER: Mehran Sharghi

PROVIDER: E-GEOD-6223 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression change induced by bisphenol A in mouse urogenital sinus

Project description:Bisphenol A (BPA), an endocrine-disrupting chemical (EDC), is a well-known, ubiquitous estrogenic chemical. To investigate the effects of fetal exposure to low-dose BPA on the development of the prostate, we first examined the alterations of in situ sex steroid hormonal environment in the mouse urogenital sinus (UGS). Next, to investigate the BPA-specific gene alterations related to increases of the E2 levels and aromatase activity, we performed comprehensive gene expression analysis using Affymetrix GeneChip in the BPA-treated or DES-treated male UGS at embryonic day 17th and postnatal day 1st. Pregnant female C57BL/6 mice were exposed to BPA (20 μg/kg/day) or synthetic estrogen Diethylstilbestrol (DES: 0.2 μg/kg/day), which were dissolved in tocopherol-stripped corn oil, on embryonic day 13 (E13) to E16. Between E17 and postnatal day 1 (P1), all animals were terminated by an overdose of isoflurane followed by cervical dislocation. Fetuses were collected at E17, E18, P0, and P1. The bladder and urethra were removed and dissected to isolate UGS and collected in RNA later. To isolate pure UGS, other tissues such as the bladder, urethra, Wolffian duct (WD), seminal vesicle (SV), and Mullerian duct (MD) were removed from both the male and female urogenital tracts. The histopathology of the mouse UGS was then examined by hematoxylin and eosin staining. Total RNA was extracted using the Qiagen mini RNA Easy kit. Each RNAs were linearly amplified and hybridized to Affymetrix GeneChip.

2010-12-06 | E-GEOD-24928 | biostudies-arrayexpress

Transcription profiling of mouse postnatal day 1 and adult bladders

2008-06-14 | E-GEOD-6466 | biostudies-arrayexpress

Transcription profiling of mouse neonatal bladder samples. (GUDMAP Series_id: 19)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder. The central thesis is straightforward. The combination of microdissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here represents the gene expression profiles of FACS sorted newborn bladder cells and compares two distinct cell populations of smooth muscle cells. Experiment Overall Design: Sorted bladder cells and bladder tissue from newborn SMGA/EGFP and SMAA/EYFP animals were microdissected or laser captured and total RNA isolated for gene expression analysis using the Affymetrix MOE430 microarray chip.

2008-06-11 | E-GEOD-11161 | biostudies-arrayexpress

Gene expression profiles of E13 bladder neck/urethral compartments (GUDMAP Series ID: 25)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder. The central thesis is straightforward. The combination of micro dissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here delineates the gene expression profiles of the mesenchymal and epithelial compartments of the E13 mouse bladder neck/urethral compartment. FVB/N mice were time mated. At embryonic day 13 mice were euthanized by decapitation and the bladders were microdissected and cut just below the ureters. Since the EDTA dissociation was ineffective, the bladder neck and urethra were collected and treated with 1 mg/ml trypsin in Tyrode's solution for 20 minutes at 37°C. The layers were separated using a fine needle and rimming. The samples were placed in RLT and stored at -80°C. RNA was prepared and the Epicentre 2-round amplification scheme described under the Lessard Group Protocols on the GUDMAP pages were performed. The amplified RNA was examined with the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

2009-04-24 | E-GEOD-15794 | biostudies-arrayexpress

Transcription profiling of mouse SMGA/EGFP adult ureter. (GUDMAP Series_id: 15)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing urogenital system. The central thesis is straightforward. The combination of microdissected and laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here represents the gene expression profiles of the adult ureter. Experiment Overall Design: Ureter regions from adult SMGA/EGFP animals were microdissected and total RNA isolated for gene expression analysis using the Affymetrix MOE430 microarray chip.

2008-06-15 | E-GEOD-7887 | biostudies-arrayexpress

Transcription profiling of mouse P7 bladder epithelium compartments: uroplakin expressing (+ve) vs. non-expressing (-ve) epithelial cells (GUDMAP Series_id: 34)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing genitourinary tract The central thesis is straightforward. The combination of microdissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here delineates the gene expression profiles of the epithelial compartments of the P7 mouse bladder. Experiment Overall Design: At postnatal day 7 mice were euthanized by CO2 asphyxiation and the bladders were removed and cut at the bladder neck. The bladder was cut into rings and treated with 1 mg/ml trypsin in TyrodeÃs solution for 30 minutes at 37 degrees C. The layers were separated by gentle microdissection and the epithelial layer was further digested in a mixture of Blendzymes1/4 at 37 degrees C until a single cell suspension was obtained The samples were placed in RLT and stored at -80 degrees C.RNA was prepared and the Epicenter 2-round amplification scheme described on the web was performed. The Affymetrix GeneChip Mouse Genome 430 2.0 Array was used to interrogate the amplified RNA.

2010-02-17 | E-GEOD-19979 | biostudies-arrayexpress

Comparison of DNA methyltransferase-1 (Dnmt1) deleted urogenital sinus epithelium compared to wildtype urogenital sinus epithelium

Project description:Dnmt1 is an important regulator of tissue development and differentiation. To assess the effects of epithelium Dnmt1 deletion in the developing urogenital sinus (precursor of the urethra and prostate in males), we isolated urogenital sinus epithelial tissue from Dnmt1 deleted mouse embryos and wildtype mouse embryos. The transcriptomes were analyzed by RNA-seq

2018-12-31 | GSE121086 | GEO

Gene expression profiles of E14 bladder, urogenital sinus and urethra isolated from SMGA (Actg2) transgenic mice. (GUDMAP Series ID: 6)

2006-11-18 | GSE6223 | GEO

Gene expression profiles of the P1 bladder isolated from SMAA-EYFP or SMAGA-EGFP (Acta2 or Actg2) transgenic and wild type mice. (GUDMAP Series ID: 2)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder. The central thesis is straightforward. The combination of laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing bladder. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in laser capture microdissected components of the developing bladder. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. As a first step we sought to determine if expression of the reporter gene (EGFP or EYFP) used to identify smooth muscle cells altered the gene expression profile of the bladder. Keywords: Comparison of postnatal day 1 bladders. Postnatal day 1 bladders were isolated from transgenic and wild-type mice to determine the effects of transgene expression on the gene expression profile in the bladder. Details of the GUDMAP project can be found at http://www.gudmap.org/index.html

2006-05-12 | E-GEOD-4816 | biostudies-arrayexpress

Gene expression profiles of E13 bladder compartments. (GUDMAP Series ID: 24)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder. The central thesis is straightforward. The combination of microdissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here delineates the gene expression profiles of the mesenchymal and epithelial compartments of the e13 mouse bladder. Keywords: Mouse embryonic day 13 bladder mesenchyme and epithelium. FVB/N mice were time mated. At embryonic day 13 mice were euthanized by decapitation and the bladders were microdissected, cut just above the ureters, and treated with 20 µM EDTA for 20 minutes. Mesenchymal and epithelial compartments were then separated by rimming the bladder with a needle and harvested in RLT. Total RNA was isolated for gene expression analysis using the Affymetrix MOE430 microarray chip

2009-01-16 | E-GEOD-12618 | biostudies-arrayexpress

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