Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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 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.

ORGANISM(S): Mus musculus

SUBMITTER: Eric Brunskill

PROVIDER: E-GEOD-21558 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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 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.

2010-05-27 | E-GEOD-21584 | 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.

2007-07-24 | E-GEOD-1983 | biostudies-arrayexpress

Gene expression in epithelial and non-epithelial cells of renal origin

Project description:We aimed to define epithelial-specific genes in the kidney. In the developing mouse kidney at E12.5 epithelial cells are restricted to the ureteric bud, while mesenchymal cells surrounding the ureteric bud are non-epithelial. The mouse renal epithelial cell line mIMCD-3 was used to represent kidney epithelia in vitro. Gene expression was analyzed using Affymetrix microarrays in ureteric bud stalks, ureteric bud tips, and mIMCD-3 cells and compared to metanephric mesenchyme. Affymetrix Mouse Genome 430 2.0 microarrays from mouse E12.5 ureteric bud tips, ureteric bus stalks, and metanephric mesenchymes had previously been published (GEO deposition: GDS1583) (Schmidt-Ott, K. M., Yang, J., Chen, X., Wang, H., Paragas, N., Mori, K., Li, J. Y., Lu, B., Costantini, F., Schiffer, M. et al. (2005). Novel regulators of kidney development from the tips of the ureteric bud. J Am Soc Nephrol 16, 1993-2002.). We added a new microarray analysis from a subclone of mIMCD-3 cells and recalculated expression values in the complete dataset by robust multichip analysis.

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

Transcription profiling of wild type and HoxA11 metenephric mesenchyme and ureteric bud from embryonic day 11.5 mice

Project description:E11.5 metanephric mesenchyme and ureteric bud were dissected from the E11.5 kidney rudiment using fine manual microdissection (ureteric bud only) or both fine manual microdissection and laser capture microdissection (metanephric mesenchyme) to define the gene expression profiles of these structures. Additionally, HoxA11, HoxD11 compound null E11.5 metanephric mesenchyme was obtained through laser capture microdissection allowing analysis of possible Hox targets in kidney development. Targets from multiple biological replicates of each were generated and the expression profiles were determined using Affymetrix MOE430_v2 arrays. Using microdissection techniques, ureteric bud and metanephric mesenchyme were dissected from E11.5 kidney rudiments allowing the identificated genes specifically regulated in either structure. In addition, Hoxa11, Hoxd11 compound null E11.5 metanephric mesenchyme were normalized to wild type embryonic controls allowing the identification of potential Hox targets in normal kidney development. Each structure/genotype were represented in biological (seperate embryo) replicate.

2007-12-07 | E-GEOD-3822 | biostudies-arrayexpress

Gene expression profiles of the E15.5 developing podocyte (GUDMAP Series_id: 33)

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.

2010-03-22 | E-GEOD-20991 | biostudies-arrayexpress

Transcription profiling of rat metanephric mesenchyme induced to convert into nephron epithelia

Project description:During kidney development segmented epithelia of the nephron derive from progenitor cells in the metanephric mesenchyme after induction by secreted molecules from the ureteric bud. We have identified three distinct inductive activities from a ureteric bud cell line. These include leukemia inhibitory factor (LIF), neutrophil gelatinase-associated lipocalin (NGAL) and an active fraction currently referred to as ANX. Each of these activities induces segmented nephron epithelia in isolated rat metanephric mesenchyme over a time period of 7 days. This study was designed to characterize the temporal sequence of gene expression in the course of the conversion process induced by each of the distinct inducers. Experiment Overall Design: Metanephric mesenchymes were microdissected from rat E13.5 embryos. Mesenchymes were cultured on transwells in the presence of either LIF, NGAL or the ANX fraction and RNA was harvested after 1, 2, 3, 4, 5, and 7 days for RNA extraction. Freshly dissected mesenchymes and mesenchymes cultured in the absence of inducers for 1 and 2 days, respectively, served as controls. Each condition was analyzed in duplicate (biological replicates). Biotinylated cRNA was prepared and hybridized to Affymetrix Rat Genome 230 2.0 Microarrays. Expression values were obtained by robust multichip analysis.

2008-06-13 | E-GEOD-5478 | 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.

2015-01-27 | E-GEOD-64959 | biostudies-arrayexpress

Gene expression profiles of the E13.5 developing podocyte (GUDMAP Series_id: 32)

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-17143 | biostudies-arrayexpress

Gene expression in epithelial and non-epithelial cells of renal origin

2010-09-23 | GSE24295 | GEO