Research Resources

The Columbia O’Brien Center serves as a resource for the urology community. We share genomic datasets via NIH repositories such as GEO, dbGaP and GUDMAP.

 

Genetic Resources

Cell Type-Specific Gene Expression Profiles in the Bladder

  • Part of the GUDMAP Project
  • Goal is to define molecular and cellular anatomy of the lower urinary tract through developmental time

Profiles of gene expression from Sall1 mutants

  • Available upon request; please contact us

Genomic data

  • CNV calls for 21,565 controls as a reference for CNV lookups
  • Raw genotyping data for RIVUR study (fully QC’ed data coming soon)

Kidney Damage (“AKI”)

  • Comparing Ischemic Damage and Volume Depletion. A Map of Gene Expression in Cortex, Glomeruli, Outer and Inner Medulla.
    • Click here for Gene List #1 and Gene List #2 (gene lists open in separate window)
    • Lists show domain-specific gene expression in damaged kidneys. These genes are upregulated >2-fold and (p<0.00001).
    • All genes that are exclusive to condition (approximately 70% of all upregulated genes) are displayed.
  • Comparing Ischemic Damage and Volume Depletion. A map of HoxB7-Cre (UB specific) and ATPase Cre (IC cell predominant) driven genes.

Gene Lists

  • Curated list of known genomic disorders
    From Verbitsky et al. J. Clin Invest 2015 (PMID 25893603) and Verbitsky et al. Nat. Genet 2019 (PMID: 30578417)
     
  • List of Genes for Mendelian Kidney and Genitourinary Disorders
    This is an expanded list of 625 Mendelian disorders that can involve the kidney and genitourinary tract developed by Hila Rasouly, Emily Groopman and Reuben Heyman-Kantor. (Rasouly et al. Ann. In Med, PMID 30476936)
     
  • List of Nephropathy Genes 
    This is the list of 287 genes for Mendelian disorders of the kidney and genitourinary tract we used in our pilot study of exome sequencing for chronic kidney disease. (Lata et al. Ann Intern Med. 2018 Jan 16;168(2):100-109, PMID: 29204651)

Mouse Models


ShhCre; Pparg Knockout Mice

  • These mice lack superficial layer

B6.Cg-Lamc2 tm1Uit /DcrJ

  • These mice lack expression of the Lamc2 gene, which encodes the β subunit of laminin 5 – a matrix glycoprotein found in basement membranes. A complete description is available from Jackson Laboratories.

Lama3 conditional knockout mouse

Cell Specific Gene Expression In Vivo

  • Uracil phosphoribosyltransferase (UPRT) was inserted into a Rosa-26 targeting vector pBigT-DEST preceded by a floxed-stop motif and followed by a transcriptional stop cassette “PGK-neo-pA-3xpA”, preventing downstream expression.
  • Because mammalian cells do not have functional UPRT, the construct directs cell-specific incorporation of 4-ThioUracil during mRNA synthesis.
  • The labeled mRNA can then be biotinylated in vitro and isolated to allow cell-specific gene expression analysis. UPRT construct from Drs. Michael Cleary and Christopher Doe.

Megalyn CreERT2-MC

  • Mouse Lrp2 is a huge gene that is over 200 kbp.
  • Using recombineering, we replaced the translational STOP (TAG) with “P2a-CreERT2-frt-neo-frt” cassette. The entire “P2a-CreERT2-frt-neo-frt” cassette as well as the 5’ and 3’ of the insertion site were completely sequenced to verify the sequencing read.
  • The resulting MC mice are maintained as homozygote. “P2a” allows expression of Lrp2 and CreERT2 from the modified allele.

Megalyn CreERT2-M5C

  • The M5C mouse was made by replacing the translational start (ATG) of Lrp2 with the“CreERT2-frt-neo-frt” cassette.
  • After removing the Neo cassette, the M5C mice are maintained as heterozygote.
  • Expression of CreERT2 in this case will inactivate Lrp2.

Tamm-Horsfall

  • TH-CreERT was also generated by inserting "P2a-CreERT2-frt-neo-frt” cassette in the 3’UTR to generate a functional TH and a functional CreERT2.

Contact the following individuals for additional information: