O’Brien Research Resources

Mouse Services

Mouse Models

• RNA-sequencing data for from Stanford University JCI Insight, 2019 publication includes: 1) bulk FFPE tissue RNA-Seq; 2) LCM dissected stroma and epithelium from BPH; 3) Single cell RNA-seq data from normal and BPH prostate; 4) whole exome sequencing of 9 BPH prostate tissues and controls. All RNA-Seq and WES data are available from the database of Genotypes and Phenotypes (https://www.ncbi.nlm.nih.gov/gap/) under phs001698.v1.p1

Source: Stanford University Urology O’Brien Center

• Tissue microarray images from Stanford University JCI Insight, 2019  publication and additional stains are available from Stanford Tissue Microarray Database (https://tma.im/cgi-bin/home.pl), as array block TA-457
• Set of tissue microarrays that contains all of the histological entities that pathologists have identified in BPH nodules. These include stromal nodules, small stromal/epithelial nodules, epithelial rich nodules of 2 different types, cystic glands and a few other morphologies. Access: email Stanford Urology O’Brien Center PI, Jim Brooks, MD for more information
• An independent set of tissue microarrays (6) that include patients with the spectrum of BPH disease and symptoms. 4 groups of patients have been targeted: small prostates, low IPSS; small prostate, high IPSS; large prostate, low IPSS; large prostate, high IPSS. New TMAs will continue to be added. The set that is available are now is being analyzed for BPH-relevant markers using MIBI. Access: email Stanford Urology O’Brien Center PI, Jim Brooks, MD for more information

Source: Stanford Urology University O’Brien Center

• Forming Consensus To Advance Urobiome Research by Brubaker et al. **The first iteration of a mixs metadata template for urobiome research is in the supplemental material.**
• International Continence Society Glossary for urology and urogynecology terms
• Mixs spreadsheet with a comprehensive collection of standard terms and definitions to use in metadata tables (this is extensive with standards for several types of samples from several environments,  we recommend first looking for a related term in the human_associated package, then the other human_ packages)
• Resource for how to enter missing values

• Methods for growing BPH and normal prostate patient derived xenografts. Stanford O’Brien Center is willing to share these methods with the urology research community, including teaching visitors to their laboratory. Access: email Stanford Urology O’Brien Center PI, Jim Brooks, MD for more information

Source: Stanford Urology University O’Brien Center

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

INSTRUCTIONAL VIDEOS

• Guide to Individual Prostate Lobe Dissection – A narrated video of mouse prostate lobe dissection. (video contains audio during dissection)
• Journey through the male mouse prostatic urethra – Serial sections of mouse prostatic urethra in the transverse plane. (no audio)
• Overview of the Spontaneous Void Spot Assay – Used to assess spontaneous voiding in unrestrained mice. (no audio)
• Overview of Cystometry – Used to assess bladder pressure associated with filling and emptying. (no audio)
• Overview of embedding prostatic urethra in transverse plane – Multiple samples are embedded in a single block to increase efficiency and increase reproducibility. (no audio)

PROTOCOLS

• Digoxigenin-11-UTP-Labeled Riboprobe Synthesis – Protocol by the Vezina Group
• 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.
• In-situ Hybridization on Vibrating Microtome-cut Mouse Tissue Sections – Protocol by the Vezina Group – PDF
• Sectioning of Paraformaldehyde-fixed Mouse Urogenital Sinus (UGS) Tissues with a Vibrating Microtome – Protocol by Vezina Group

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

• Digoxigenin-labeled in-situ hybridization of urogenital sections – Protocol here PDF
• Riboprobe synthesis from a plasmid template – Protocol here PDF

OTHER

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

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