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-- Transcriptomic and Proteomic Databases 

 


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Epithelial Systems Biology Laboratory

Mark A. Knepper, MD, PhD, Principal Investigator

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1) Transcriptomic Databases for Native Kidney Epithelia

                     Rat Proximal Tubule Transcriptome (Click for reference)

                                                       

                      Rat Thick Asc. Limb Transcriptome                                    Rat IMCD Transcriptome

                              (Click for reference                                                       (Click for reference)

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2) Transcriptomic Database for Cultured Epithelial Cells

Mouse mpkCCD (Clone 11 vs Clone 2) Transcriptome
Lists all transcripts identified in cultured mouse mpkCCD clonal cell lines based on Affymetrix array profiling (from: Yu et al. Proc Natl Acad Sci U S A. 2009; 106: 2441-6). 
 

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3) Proteomics Databases for Native Kidney Epithelia

IMCD Proteome Database
Lists all proteins identified in native IMCD cells from rats using protein mass spectrometry.

Collecting Duct Phosphoprotein Database (CDPD)
Lists all phosphoproteins and specific sites of phosphorylation for native rat IMCD cells determined by protein mass spectrometry.

Rat IMCD Phosphoproteome Database
Lists all phosphoproteins and specific sites of phosphorylation for native rat IMCD cells determined by protein mass spectrometry (CDPD udated with data from Bansal et al. accepted by JASN).
 

Inner Medullary Collecting Duct Membrane Protein (IMP) Database
Lists all integral and GPI-anchored membrane proteins identified in native IMCD cells from rats using protein mass spectrometry.

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4) Proteomics Database for Human Urinary Exosomes

Human Urinary Exosome Database
Lists all proteins identified in exosomes isolated from urine using protein mass spectrometry. (From: Pisitkun et al. Proc Natl Acad Sci U S A. 2004; 101: 13368-73 and Gonzales et al. J. Am. Soc. Neprhol. 2009; 20: 363-79.)

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5) Proteomics Databases for Papers under Review

(password protected)

Mouse mpkCCD Phosphoproteome Database
Lists all phosphoproteins and specific sites of phosphorylation for cultured mouse mpkCCD cells (NHLBI-clone 11)determined by protein mass spectrometry.

Mouse Kidney and Epididymal V-ATPase-Rich Cell Proteome Database
Lists all proteins found by LC-MS/MS analysis of flow-sorted GFP positive cells from the kidneys of mice expressing GFP under the control of the 5'-flanking region of the mouse B1-subunit of the vacuolar H-ATPase. 

  

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