Oct 21, 2022
Protocols for Molecular Characterization of the Female Reproductive System
- Stephen Fisher1,
- Marielena Grijalva1,
- Rong Guo1,
- sarahjoh 1,
- Hieu Nguyen1,
- John Renz2,
- Steven Rudich2,
- Brian Gregory1,
- Junhyong Kim1,
- Kate O'Neill1,
- Jean G Rosario1
- 1University of Pennsylvania;
- 2Gift of Life Donor Program
- Kate O'Neill: corresponding author;
- Human BioMolecular Atlas Program (HuBMAP) Method Development CommunityTech. support email: [email protected]
Protocol Citation: Stephen Fisher, Marielena Grijalva, Rong Guo, sarahjoh , Hieu Nguyen, John Renz, Steven Rudich, Brian Gregory, Junhyong Kim, Kate O'Neill, Jean G Rosario 2022. Protocols for Molecular Characterization of the Female Reproductive System. protocols.io https://dx.doi.org/10.17504/protocols.io.kqdg3pj37l25/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: July 27, 2022
Last Modified: October 21, 2022
Protocol Integer ID: 67668
Keywords: ATACseq, RNAseq, Visium, ovary, Fallopian tube, uterus, comprehensive molecular characterization of the female reproductive system, female reproductive cell, 10x genomics multiome, structure of female reproductive cell, female reproductive system, individual diversity of the female reproductive system, 10x genomics visium platform, human biomolecular atlas program, 10x genomic, genomic, protocols for molecular characterization, comprehensive molecular characterization, functional characteristics of the uterus, structured tissue sampling procedure, fallopian tube, molecular characterization
Funders Acknowledgements:
NIH
Grant ID: U54HD104392
Abstract
Here we describe our multi-step protocol to generate a comprehensive molecular characterization of the female reproductive system. We begin with organ procurement that maintains functional characteristics of the uterus, ovaries, and Fallopian tubes and then describe our structured tissue sampling procedure that represents anatomical, physiological, and individual diversity of the female reproductive system, toward full exploration of the function and structure of female reproductive cells.
These protocols were developed as part of the National Institutes of Health (NIH) Human BioMolecular Atlas Program (HuBMAP), we are centered around the 10X Genomics Multiome and 10X Genomics Visium platforms.
Troubleshooting
Overview of Protocols. Graphic overview of the order and processing employed by HuBMAP’s Tissue Mapping Center at Penn to create a 3D molecular map of the female reproductive system.
Preparation and Preservation of the Female Reproductive System (ovaries, Fallopian tubes and uterus) Prior to Procurement
Removal of the Female Reproductive SystemEn Bloc
Post-Surgical Dissection of Ovaries
Post-Surgical Dissection of Fallopian Tubes
Post-Surgical Dissection of Cervix
Post-Surgical Dissection of Uterine Body
Tissue Slice Preparation for Visium Analysis
Manual Tissue Dissociation for Multiome Analysis
Tissue Dissociation for Multiome Analysis Using S2 Singulator