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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiles of an E10.5 ureteric duct cell (GUDMAP Series_id: 40)

ABSTRACT: The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. 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. HoxB7-GFP transgenic mice were utilized to isolate the ureteric duct cells from E10.5 embryonic kidneys. The ureteric duct cells were isolated from embryos using microdissection, trypsin treatment and FACS. The RNA was isolated from purified ureteric duct cells and the gene expression profiles were determined by microarrays.

ORGANISM(S): Mus musculus

SUBMITTER: Eric Brunskill

PROVIDER: E-GEOD-21584 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profiles of E10.5 ureteric bud cells. (GUDMAP Series_id: 39)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. 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. HoxB7-GFP transgenic mice were utilized to isolate the ureteric bud cells from E10.5 embryonic kidneys. The ureteric bud cells were isolated from embryos using microdissection, trypsin treatment and FACS. The RNA was isolated from purified ureteric bud cells and the gene expression profiles were determined by microarrays.

2010-05-27 | E-GEOD-21558 | biostudies-arrayexpress

RNA-SEQ analysis of various developing and adult kidney components.

Project description:We used micro-dissection techniques and/or FACS to isolate cell types from the developing and adult kidney (E11.5 ureteric buds, E12.5, P1 and P4 cap mesenchyme, E15.5 collecting ducts, proximal tubules, ureter, Adult renal proximal tubules, podocytes, endothelial and mesangial cells). RNA-SEQ analysis was performed to determine the transcriptional profile of each cell type, identify component specific transcripts and isoforms and cell-type specific long-noncoding RNAs. In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database. Total RNA is obtained from micro-dissected and/or FACS isolated embryonic and adult kidney components. The long term goal is to generate a transcriptional atlas of developing kidney.

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Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. 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. MafB-GFP BAC transgenic mice were utilized to isolate the podocyte cells from the developing embryonic kidneys. Podocyte cells were isolated from the kidney using trypsinization and FACS. RNA was isolated and the gene expression profiles were determined by microarrays.

2010-07-16 | E-GEOD-17145 | biostudies-arrayexpress

Gene expression profiles of E15.5 endothelial cells (GUDMAP Series_id: 38)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. 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. Tie2-GFP transgenic mice were utilized to isolate the endothelial cell population from E15.5 embryonic kidneys. The endothelial cells were isolated from embryos using trypsin treatment and FACS. The RNA was isolated from purified endothelial cells and the gene expression profiles were determined by microarrays.

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2010-07-16 | E-GEOD-17143 | biostudies-arrayexpress

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2010-09-23 | E-GEOD-24295 | biostudies-arrayexpress

Transcription profiling of initial stages of metanephric development in mouse and rat

Project description:In this study we identify molecules with highly restricted expression patterns during the initial stages of metanephric development, when the ureteric bud has entered the metanephric mesenchyme and initiated branching morphogenesis. Using the Affymetrix Mouse Genome 430 2.0 Array, we compare gene expression patterns in ureteric bud tips, stalks and metanephric mesenchymes from mouse E12.5 embryos. To identify conserved molecular pathways, we also analyze transcriptional profiles in rat E13.5 ureteric buds and metanephric mesenchymes using the Affymetrix Rat Genome U34 Set. Taken together, these data sets help to identify conserved and highly localized transcripts in the metanephric kidney.

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mRNA-Seq profile of gene expression in tip and stalk compartments of ureteric epithelium in developing mouse kidney

Project description:Morphogenesis of cellecting duct system within developing mouse kidney is driven by growth at the tips of ureteric epithelium. To characterize the transcription program within the tip compartment, here we performed mRNA-Seq of tip cells (Wnt11RFP+;Hoxb7+ cells) and stalk cells (Wnt11RFP-;Hoxb7GFP+ cells) obtained from mouse embryonic kidney through FACS. We identified tip-specific genes from these data, and verified with in situ hybridization and followed up with mechanistic study for some of the intersting targets.

2017-08-15 | GSE93267 | GEO

Gene expression profiles of the cap mesenchyme & renal vesicle in the neonatal kidney (GUDMAP Series_id: 28)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. 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. At E18.5, pups were isolated from CRYM-BAC transgenic mice and fostered to CD-1 mice. Cap mesenchyme cells were isolated from the kidney by fluorescent activated cell sorting (FACS) on postnatal days 0, 1, 2, 3, and 4. RNA was isolated from FACS sorted cells and the gene expression profiles were determined by microarrays.

2010-07-16 | E-GEOD-17139 | biostudies-arrayexpress

Gene expression profiles of the adult capsular cell (GUDMAP Series_id: 36)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. 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. CD-1 mice were utilized to isolate the capsule cells from the adult kidneys. The capsule cells were isolated from the kidney using microdissection treatment. RNA was isolated and the gene expression profiles were determined by microarrays.

2010-03-05 | E-GEOD-20639 | biostudies-arrayexpress

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