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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Data Processing and Preparation of MALDI IMS data Resource Report Resource Website |
Nathan Heath Patterson, Elizabeth Neumann, Jamie Allen, Danielle Gutierrez, Jeff Spraggins | 10.17504/protocols.io.bed3ja8n | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:How to process a mass spectrometry imaging data into a final imzML file. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 1 | 2020 | Nathan Heath Patterson, Elizabeth Neumann, Jamie Allen, Danielle Gutierrez, Jeff Spraggins 2020. Data Processing and Preparation of MALDI IMS data. protocols.io dx.doi.org/10.17504/protocols.io.bed3ja8n | 2021-03-29 03:14:23 | |||
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HuBMAP: Embedding Fresh Frozen OCT Samples Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick | 10.17504/protocols.io.bcwsixee | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the OCT embedding of HuBMAP fresh frozen specimens. | university of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Jerelyn Nick 2020. HuBMAP: Embedding Fresh Frozen OCT Samples. protocols.io dx.doi.org/10.17504/protocols.io.bcwsixee | 2021-03-29 03:14:52 | |||
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UF / HuBMAP - H&E Staining Process Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen, Leigh Propper | 10.17504/protocols.io.9qbh5sn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This protocol will detail our method of utilizing the H&E stain as a nonspecific entity to achieve optimal results in our staining process for our research samples.Hematoxylin and Eosin stains are used in many areas of the laboratory, including frozen sections, fine needle aspirates, and paraffin fixed embedded tissues. There are multiple factors involved in determining what makes a well stained slide, and one of the primary factors involved in the final product is pathologist preference. Other important factors also play important roles in your final stain, such as reagents and their quality, consistency, initial microtomy quality and selecting a sound procedure. Hematoxylin is used to illustrate nuclear detail in cells. The resulting intensity and shade of the dye in the cells is primarily reliant on the length of time the sample spends in hematoxylin. The cytoplasmic component of the section is brought out by Eosin, which is the most commonly used counterstain in histology. It's varying shades of pink and red provide an exceptional contrast between the nuclear and cytoplasmic areas of interest. | University of Florida, University of Florida, University of Florida | 2 | 2019 | Franchesca Farris, Marda Jorgensen, Leigh Propper 2019. UF / HuBMAP - H&E Staining Process . protocols.io dx.doi.org/10.17504/protocols.io.9qbh5sn | 2021-03-29 03:15:05 | |||
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Cell DIVE™ Platform | Antibody Staining & Imaging Resource Report Resource Website |
Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood | 10.17504/protocols.io.bpv6mn9e | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | This document outlines the workflow for antibody staining, dye inactivation, and imaging as per the Cell DIVE™ technology. | GE Research, GE Research, GE Research, GE Research, GE Research | 1 | 2020 | Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood 2020. Cell DIVE™ Platform | Antibody Staining & Imaging. protocols.io dx.doi.org/10.17504/protocols.io.bpv6mn9e | 2021-03-29 03:15:16 | |||
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Appendix for Spleen SOP Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick | 10.17504/protocols.io.bbcviiw6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This is an appendix diagram for spleen tissue cutting. | university of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Jerelyn Nick 2020. Appendix for Spleen SOP. protocols.io dx.doi.org/10.17504/protocols.io.bbcviiw6 | 2021-03-29 03:15:09 | |||
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HubMap UF TMC Tissue Dissociation to Single Cell Resource Report Resource Website |
Marda Jorgensen, Maigan Brusko | 10.17504/protocols.io.bd9vi966 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Maigan Brusko 2020. HubMap UF TMC Tissue Dissociation to Single Cell. protocols.io dx.doi.org/10.17504/protocols.io.bd9vi966 | 2021-03-29 03:15:24 | ||||
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Freezing Fresh Tissue Resource Report Resource Website |
Jamie Allen, Maya Brewer, Elizabeth Neumann, Danielle Gutierrez, Mark deCaestecker, Jeff Spraggins | 10.17504/protocols.io.6wghfbw | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:To describe the procedure for freezing fresh tissue procured from the Cooperative Human Tissue Network.Expected Outcome:Frozen tissue should have minimal structural damage from freezing. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University Medical Center, Vanderbilt University | 2 | 2019 | Jamie Allen, Maya Brewer, Elizabeth Neumann, Danielle Gutierrez, Mark deCaestecker, Jeff Spraggins 2019. Freezing Fresh Tissue. protocols.io dx.doi.org/10.17504/protocols.io.6wghfbw | 2021-03-29 03:12:12 |
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