Collaborating for the Advancement of Interdisciplinary Research in Benign Urology

Research Resources

O’Brien Center Resources

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TISSUE STAINING

Resource Details Access Source
Immunohistochemistry (IHC) for In-situ Hybridization (ISH)-stained Mouse Sections Intended for 50-80 micron free-floating mouse tissue sections that were ISH-stained with BM Purple and post-fixed in 4%. All washing steps should be performed with gentle agitation on an orbital shaker GUDMAP University of Wisconsin-Madison O'Brien Center
In-situ Hybridization on Vibrating Microtome-cut Mouse Tissue Sections Protocol by the Vezina Group GUDMAP; PDF University of Wisconsin-Madison O'Brien Center
Paraffin Section IHC Protocol Protocol for fluorescent immunostaining of formlin-fixed, paraffin-embedded tissue sections PDF University of Wisconsin-Madison O'Brien Center
Whole Mount IHC Protocol Protocol for whole mount immunohistochemistry of tissue PDF University of Wisconsin-Madison O'Brien Center
IHC Protocol IHC tissue staining protocol PDF University of Pittsburgh O’Brien Center
Immunofluorescent staining of fixed frozen tissue Find protocols within the CBI website by clicking “Protocols” at the top right-hand corner Center for Biologic Imaging University of Pittsburgh O’Brien Center
Live cell imaging Find protocols within the CBI website by clicking “Protocols” at the top right-hand corner Center for Biologic Imaging University of Pittsburgh O’Brien Center
Digoxigenin-labeled in-situ hybridization of urogenital sections This protocol is for digoxigenin-labeled in-situ hybridization of urogenital sections GUDMAP; PDF Columbia University O’Brien Center

TISSUE EMBEDDING

Resource Details Access Source
Overview of embedding prostatic urethra in transverse plane Multiple samples are embedded in a single block to increase efficiency and increase reproducibility. (no audio) GUDMAP University of Wisconsin-Madison O'Brien Center
Tissue Embedding Protocol Step-by-step protocol for embedding tissue in paraffin for sectioning PDF University of Wisconsin-Madison O'Brien Center
Epoxy resin or acrylic Find protocols within the CBI website by clicking “Protocols” at the top right-hand corner Center for Biologic Imaging University of Pittsburgh O’Brien Center
Frozen samples for cryo sectioning for immunoTEM Find protocols within the CBI website by clicking “Protocols” at the top right-hand corner Center for Biologic Imaging University of Pittsburgh O’Brien Center

CELL MOVEMENT AND PERMEABILITY

Resource Access Source
FITC-dextran transwell assay Here University of Pittsburgh O’Brien Center
TER measurment Here University of Pittsburgh O’Brien Center

ELECTRON MICROSCOPY PREPARATION

Resource Details Access Source
Backscatter analysis Find protocols within the CBI website by clicking “Protocols” at the top right-hand corner Center for Biologic Imaging University of Pittsburgh O’Brien Center
SEM monolayer, cell, tissue processing Find protocols within the CBI website by clicking “Protocols” at the top right-hand corner Center for Biologic Imaging University of Pittsburgh O’Brien Center
SEM monolayer, cell, tissue processing Find protocols within the CBI website by clicking “Protocols” at the top right-hand corner Center for Biologic Imaging University of Pittsburgh O’Brien Center

OTHER PROTOCOLS

Resource Details Access Source
Digoxigenin-11-UTP-Labeled Riboprobe Synthesis Protocol by the Vezina Group GUDMAP University of Wisconsin-Madison O'Brien Center
Sectioning of Paraformaldehyde-fixed Mouse Urogenital Sinus (UGS) Tissues with a Vibrating Microtome Protocol by the Vezina Group GUDMAP University of Wisconsin-Madison O'Brien Center
Riboprobe synthesis from a plasmid template Protocol GUDMAP Columbia University O’Brien Center
Patient-derived explant (PDE) Patient-derived explant of prostate tissue PDF University of Pittsburgh O’Brien Center
3D Culture Protocol Primary BPH stromal cell culture and prostatic epithelial 3D culture PDF University of Pittsburgh O’Brien Center

VALIDATED ANTIBODIES

Resource Details Access Source
Benign Prostate Research Antibodies List of validated antibodies useful in benign prostate research PDF University of Wisconsin-Madison O'Brien Center

MOUSE SERVICES AND MODELS

MOUSE SERVICES

  • Rodent Urinary Function Testing (RUFT) Core – The RUFT Core designs, validates, and disseminates protocols for rodent urinary function testing. They also provide urinary function testing services using our state-of-the-art equipment. The RUFT Core provides expertise, laboratory space, vivarium, and equipment for complete mouse urinary function testing. Fee-for-service.

Source: University of Wisconsin-Madison O’Brien Center

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  • Inducible prostate-specific Cdh1 KO mice – ACCESS: Wang Lab 
  • Rodent urodynamic testing – ACCESS: Yoshmura Lab

Source: University of Pittsburgh O’Brien Center

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Mouse Models

Name Details Access Source
Barasch Hmox1f/f NA - Barasch Lab; Email Columbia University O’Brien Center
Barasch Hmox1-luc Hemoxygenase reporter mice Gift of Anupam Argawaal Barasch Lab; Email Columbia University O’Brien Center
Barasch Rosa26mTmGf/+ - Barasch Lab; Email Columbia University O’Brien Center
Barasch Lcn2f/f - JAX Columbia University O’Brien Center
Barasch Lcn2-Luciferase - JAX Columbia University O’Brien Center
Barasch Slc40a1f/f Gift of Nancy Andrews JAX Columbia University O’Brien Center
Barasch Slc48a1f/f Gift of Iqbal Hamza JAX Columbia University O’Brien Center
Barasch Tfcp2l1f/f - JAX Columbia University O’Brien Center
Barasch Tfr1f/f - JAX Columbia University O’Brien Center
Barasch Uprt f/f - JAX Columbia University O’Brien Center
Mendelsohn B6.Cg Shhtm1(EGFP/cre)Cjt/J ShhCre Stock# 005622 JAX Columbia University O’Brien Center
Mendelsohn B6;CBA-Tg(Upk2-icre/ERT2)1Ccc/J Upk2CreERT2 Stock# 024768 JAX Columbia University O’Brien Center
Mendelsohn Gt(ROSA)26Sortm4 R26RmTmG Stock# 007576 JAX Columbia University O’Brien Center
Mendelsohn PpargtmGonz; Pparg Gift of Frank Gonzalez NIH Columbia University O’Brien Center
Mendelsohn Tg(Krt5-Cre/ERT2)2lpc/J Krt5CreERT2 - IGBMC Columbia University O’Brien Center

SOFTWARE, CODING, AND DATA TOOLS

Resource Access Source
Cellranger analysis count workflow Zenodo University of Wisconsin-Madison O'Brien Center
Cellranger analysis mkfastq workflow Zenodo University of Wisconsin-Madison O'Brien Center
Human and mouse prostate and urethra scRNA-seq and IHC raw data and images GUDMAP University of Wisconsin-Madison O'Brien Center
scRNA-seq analysis pipeline Zenodo University of Wisconsin-Madison O'Brien Center

DATASETS

Dataset Details Access Source
GSE107585 Comprehensive single cell RNAseq analysis of the kidney; Reveals novel cell types and unexpected cell plasticity GEO Columbia University O’Brien Center
GSE87752 Genome wide map of Tfcp2l1 binding sites from mouse kidney GEO Columbia University O’Brien Center
GSE135868 Heme metabolism confronts urinary pathogens at the urothelium; Whole Urothelium GEO Columbia University O’Brien Center
GSE87769 Identification of Tfcp2l1 target genes in the mouse kidney GEO Columbia University O’Brien Center
GSE85491 Krt5+ uninfected/Krt5+ infected; Cells sorted from K5CreERT2;mTmG mice infected with UTI 898 OR UNINFECTED GEO Columbia University O’Brien Center
GSE62310 RNA-SEQ analysis of the developing lower urogenital region GEO Columbia University O’Brien Center
GSE87744 RNA-Seq gene expression analysis in rat metanephric mesenchyme; Overexpresses transcription factor Tfcp2I1 GEO Columbia University O’Brien Center
GSE85491 RNA-Seq of superficial, intermediate and basal layers of urothelium GEO Columbia University O’Brien Center
GSE85325 Tfcp2l1 controls cellular patterning of the collecting duct GEO Columbia University O’Brien Center
GSE81741 Unique transcriptional programs identify subtypes of AKI GEO Columbia University O’Brien Center
GSE62310 Urothelium; E12.5 & E17.5 GEO Columbia University O’Brien Center
GSE62310 Urothelium; E18 Krt5+. Urothelium sorted from ShhCre;mTmG embryos E12.5 and E17.5 GEO Columbia University O’Brien Center
GSE62310 Urothelium; P5 Upk+. Urothleial cells sorted from Upk2CreErt2mTmG mice at P5 GEO Columbia University O’Brien Center
GSE123779 WT and K5CreER; Pparg (+/-,fl/fl); Sorted basal cells under homeostasis GEO Columbia University O’Brien Center
GSE123779 WT and K5CreER; Pparg (+/-,fl/fl); Sorted basal cells after UTI GEO Columbia University O’Brien Center
GSE123779 WT and ShhCre;Pparg (+/-, fl/fl); Whole urothelium under homeostasis GEO Columbia University O’Brien Center
GSE123779 WT and ShhCre;Pparg (+/-, fl/fl); Whole urothelium after UTI GEO Columbia University O’Brien Center
Phs001749.v1.p1 Microarray data from >1000 patients with CAKUT and urogenital disorders NCB dbGAP Columbia University O’Brien Center

SPECIMENS

Resource Details Access Source
Human prostate scRNA-seq data visualization - Strand Lab University of Wisconsin-Madison O'Brien Center
Mouse prostate scRNA-seq data visualization - Strand Lab University of Wisconsin-Madison O'Brien Center
>200 human bladder FFPE/OCT blocks - Strand Lab University of Wisconsin-Madison O'Brien Center
>500 human prostate FFPE blocks, >300 human prostate OCT blocks - Strand Lab University of Wisconsin-Madison O'Brien Center
Sequenced Urinary Bacteria in Microbial Genomics Biomedical Core Sampling of urinary bacteria collected by Dr. Anne-Catrin Uhlemann; all sequenced, curated, and housed in her lab Microbial Genomics Biomedical Core Columbia University O’Brien Center
Cystoprostatectomy specimens BPH; 587 cases; fee for services Dr. Rajiv Dhir University of Pittsburgh O’Brien Center
Cystoprostatectomy specimens Normal; 406 cases; fee for services Dr. Rajiv Dhir University of Pittsburgh O’Brien Center
Donor Normal prostates 376 cases; fee for services Dr. Rajiv Dhir University of Pittsburgh O’Brien Center
Simple/ retropubic prostatectomy specimens BPH; 45 cases; fee for services Dr. Rajiv Dhir University of Pittsburgh O’Brien Center
TURP specimens BPH; 825 cases; fee for services Dr. Rajiv Dhir University of Pittsburgh O’Brien Center

GUDMAP RESOURCES

University of Wisconsin-Madison George M. O’Brien Urology Center

INSTRUCTIONAL VIDEOS

PROTOCOLS

OTHER

  • GUDMAP antibody repositories, antibody media files, antibody tests, collections, images, and specimens from Chad Vezina, PhD here.
  • GUDMAP collections, experiments, files, images, replications, scRNA files, single cell metrics, specimens, studies, and study analysis files from Douglas Strand, PhD here.

GUDMAP Contributors from UW-Madison U54 O’Brien Center: Chad Vezina, PhD; Douglas Strand, PhD

Columbia University George M. O’Brien Urology Center

PROTOCOLS

OTHER

  • GUDMAP antibody repositories, experiments, files, images, replications, specimens, and studies from Cathy Mendelsohn, PhD here.

GUDMAP Contributor from Columbia University U54 O’Brien Center: Cathy Mendelsohn, PhD