Collaborating for the Advancement of Interdisciplinary Research in Benign Urology

RESOURCES

O’Brien Center Resources

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TISSUE STAINING

Source: University of Wisconsin-Madison O’Brien Center

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*Find protocols within the CBI website by clicking “Protocols” at the top right-hand corner

Source: University of Pittsburgh O’Brien Center

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Source: Columbia University O’Brien Center

TISSUE EMBEDDING

Source: University of Wisconsin-Madison O’Brien Center

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*Find protocols within the CBI website by clicking “Protocols” at the top right-hand corner

Source: University of Pittsburgh O’Brien Center

CELL MOVEMENT AND PERMEABILITY

Source: University of Pittsburgh O’Brien Center

ELECTRON MICROSCOPY PREPARATION

*Find protocols within the CBI website by clicking “Protocols” at the top right-hand corner

Source: University of Pittsburgh O’Brien Center

OTHER PROTOCOLS

Source: University of Wisconsin-Madison O’Brien Center

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Source: Columbia University O’Brien Center

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Source: University of Pittsburgh O’Brien Center

VALIDATED ANTIBODIES

Benign Prostate Research Antibodies – List of validated antibodies useful in benign prostate research

Source: 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

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

Source: Columbia University O’Brien Center

SOFTWARE, CODING, AND DATA TOOLS

DATASETS

DATASETS

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

Source: Columbia University O’Brien Center

SPECIMENS

Source: University of Wisconsin-Madison O’Brien Center

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  • 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 (ACCESS: Microbial Genomics Biomedical Core)

Source: Columbia University O’Brien Center

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  • Cystoprostatectomy specimens (BPH): 587 cases (fee for services; ACCESS: Dr. Rajiv Dhir)
  • Cystoprostatectomy specimens (Normal): 406 cases (fee for services; ACCESS: Dr. Rajiv Dhir)
  • Donor Normal prostates: 376 cases (fee for services; ACCESS: Dr. Rajiv Dhir)
  • Simple/ retropubic prostatectomy specimens (BPH): 145 cases (fee for services; ACCESS: Dr. Rajiv Dhir)
  • TURP specimens (BPH): 825 cases (fee for services; ACCESS: Dr. Rajiv Dhir)

Source: 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

General Resources

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GRANT WRITING

NIH RESOURCES

  • Getting started? Watch this video that covers the basics of the NIH grants process
  • Find example applications here including R01, R03 and K01 grants
  • What grant is right for you? Read more here
  • Already funded? Find tips to stay funded
  • Search funding or find similarly funded projects with the NIH’s RePORTER Matchmaker tool
  • All About Grants Podcast: Considerations for a Research Plan
    • Thanks to a suggestion from a listener, in this NIH All About Grants episode a duo of NIH program officers, Drs. Lillian Kuo from the National Cancer Institute and Kentner Singleton from the National Institute of Allergy and Infectious Diseases, share their advice and experience on developing a research plan for a grant application. They discuss the relationship between the specific aims and research strategy, provide suggestions for when you sit down to start writing, and share common pitfalls.
  • Ever Wondered What Happens During the Scientific Review of an NIH Grant Application?
    • Understanding how peer review works is key to writing a good grant application.  In this 44-minute video, NIH Peer Review: “Live” Mock Study Section, scientists have gathered virtually to review three fictional applications in response to a fictional Request For Applications.

GRANTS.GOV

  • Learn the basics of grants including the grant lifecycle, grant policies, grant terminology, and more

OTHER PROPOSAL WRITING RESOURCES

Source: Office of Research and Sponsored Program, University of Northern Colorado

 

OTHER RESOURCES

 Connect to online resources

 

Tips and tricks for giving “flash talk” poster presentations at scientific meetings