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Authors: Nathan Heath Patterson, Elizabeth Neumann, Jamie Allen, Danielle Gutierrez, Jeff Spraggins
Group: VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: Scope:How to process a mass spectrometry imaging data into a final imzML file.
Proper citation: 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 Copy
Authors: Marda Jorgensen, Jerelyn Nick
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the OCT embedding of HuBMAP fresh frozen specimens.
Proper citation: Marda Jorgensen, Jerelyn Nick 2020. HuBMAP: Embedding Fresh Frozen OCT Samples. protocols.io dx.doi.org/10.17504/protocols.io.bcwsixee Copy
Authors: Franchesca Farris, Marda Jorgensen, Leigh Propper
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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.
Proper citation: Franchesca Farris, Marda Jorgensen, Leigh Propper 2019. UF / HuBMAP - H&E Staining Process . protocols.io dx.doi.org/10.17504/protocols.io.9qbh5sn Copy
Authors: Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research
Summary: This document outlines the workflow for antibody staining, dye inactivation, and imaging as per the Cell DIVE™ technology.
Proper citation: 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 Copy
Authors: Marda Jorgensen, Jerelyn Nick
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This is an appendix diagram for spleen tissue cutting.
Proper citation: Marda Jorgensen, Jerelyn Nick 2020. Appendix for Spleen SOP. protocols.io dx.doi.org/10.17504/protocols.io.bbcviiw6 Copy
Authors: Marda Jorgensen, Maigan Brusko
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Proper citation: Marda Jorgensen, Maigan Brusko 2020. HubMap UF TMC Tissue Dissociation to Single Cell. protocols.io dx.doi.org/10.17504/protocols.io.bd9vi966 Copy
Authors: Jamie Allen, Maya Brewer, Elizabeth Neumann, Danielle Gutierrez, Mark deCaestecker, Jeff Spraggins
Group: VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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.
Proper citation: 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 Copy
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