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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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High Resolution Imaging Mass Spectrometry Analysis using Bruker Daltonics Platforms Resource Report Resource Website |
Elizabeth Neumann, Jamie Allen, David Anderson, Danielle Gutierrez, Jeff Spraggins | DOI:10.17504/protocols.io.7gdhjs6 | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:Acquire 10 μm spatial resolution imaging mass spectrometry (IMS) datasets of ~ 5mm2 regions of tissue.Expected Outcome:A series of ion images that can be used to visualize the distribution of lipids localizing to physiological regions within the human kidney. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 1 | 2019 | Elizabeth Neumann, Jamie Allen, David Anderson, Danielle Gutierrez, Jeff Spraggins 2019. High Resolution Imaging Mass Spectrometry Analysis using Bruker Daltonics Platforms. protocols.io https://dx.doi.org/10.17504/protocols.io.7gdhjs6 | 2021-04-15 09:15:23 | |||
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HuBMAP TMC-Florida/Zurich CODEX Modality Overview Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick, Franchesca Farris, Jesus Penaloza | DOI:10.17504/protocols.io.be9pjh5n | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This protocol is an overview of all of the protocols currently in use for the CODEX modality at HubMAP Tissue Mapping Center,TMC-Florida/Zurich. It includes protocols.io links to each of the individual protocols that make up this project workflow, from processing tissue and imaging the samples, to uploading the final data to the HuBMAP HIVE. | University of Florida, University of Florida, University of Florida, University of Florida | 2 | 2020 | Marda Jorgensen, Jerelyn Nick, Franchesca Farris, Jesus Penaloza 2020. HuBMAP TMC-Florida/Zurich CODEX Modality Overview. protocols.io https://dx.doi.org/10.17504/protocols.io.be9pjh5n | 2021-04-15 09:15:27 | |||
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PAS Staining of Fresh Frozen or Paraffin Embedded Human Kidney Tissue Resource Report Resource Website |
Jamie Allen, Jennifer Harvey, Maya Brewer, Mark De Caestecker, Jeff Spraggins | DOI:10.17504/protocols.io.4qngvve | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:The PAS stain is used to demonstrate polysaccharides such as glycogen, and mucosubstances such as glycoproteins, glycolipids and mucins in tissues. It is used as a replacement for the H&E in kidney pathology.Expected Outcome:Intermyofibrillar Network…………………………..Pink to RoseGlycogen………………………………………………….…..Pink to RoseMyofibrils……………………………………………………..UnstainedType I fibers………………………………………………….LighterType II fibers…………………………………………………DarkerBlood Vessel walls & connective tissue…..Faintly Stained | Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center, Division of Nephrology, Vanderbilt University Medical Center, Vanderbilt University | 1 | 2019 | Jamie Allen, Jennifer Harvey, Maya Brewer, Mark De Caestecker, Jeff Spraggins 2019. PAS Staining of Fresh Frozen or Paraffin Embedded Human Kidney Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.4qngvve | 2021-04-15 09:15:48 | |||
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Coverslips preparation for seqFISH Resource Report Resource Website |
Nina Dar, Long Cai, Shin Lin | DOI:10.17504/protocols.io.7mihk4e | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | California Institute of Technology, California Institute of Technology, University of Washington | 1 | 2019 | Nina Dar, Long Cai, Shin Lin 2019. Coverslips preparation for seqFISH . protocols.io https://dx.doi.org/10.17504/protocols.io.7mihk4e | 2021-04-15 09:15:36 | ||||
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Collection and Post-Surgical Excision of Human Kidney Tissue through the Cooperative Human Tissue Network Resource Report Resource Website |
Maya Brewer, Jamie Allen, Elizabeth Neumann, Agnes Fogo, Raymond Harris, Danielle Gutierrez, Mark De Caestecker, Jeff Spraggins | DOI:10.17504/protocols.io.7gehjte | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:Obtain kidney tissue and metadata about tissue location within the whole kidney for storage and analysis.Expected Outcome:A portion of kidney tissue and a series of images that provide information about the original location of the smaller tissue. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University Medical Center, Vanderbilt University Medical Center, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center, Vanderbilt University | 1 | 2019 | Maya Brewer, Jamie Allen, Elizabeth Neumann, Agnes Fogo, Raymond Harris, Danielle Gutierrez, Mark De Caestecker, Jeff Spraggins 2019. Collection and Post-Surgical Excision of Human Kidney Tissue through the Cooperative Human Tissue Network. protocols.io https://dx.doi.org/10.17504/protocols.io.7gehjte | 2021-04-15 09:15:43 | |||
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SOP Appendix for Lymph Node Resource Report Resource Website |
Marda Jorgensen | DOI:10.17504/protocols.io.bcwpixdn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This is the appendix for lymph nodes. | University of Florida | 1 | 2020 | Marda Jorgensen 2020. SOP Appendix for Lymph Node. protocols.io https://dx.doi.org/10.17504/protocols.io.bcwpixdn | 2021-04-15 09:15:47 | |||
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Case Processing SOP (Spleen) Resource Report Resource Website |
Marda Jorgensen | DOI:10.17504/protocols.io.bc3kiykw | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The purpose of this Standard Operating Procedure is to outline procedures for processing and storing spleen received for HuBMAP consortium assay and analysis. | University of Florida | 3 | 2020 | Marda Jorgensen 2020. Case Processing SOP (Spleen). protocols.io https://dx.doi.org/10.17504/protocols.io.bc3kiykw | 2021-04-15 09:15:53 | |||
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CODEX Acquisition Protocol Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen, Jerelyn Nick, Jesus Peñaloza | DOI:10.17504/protocols.io.bdifi4bn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Multiplex imaging of lymph node, thymus and spleen is accomplished using the Akoya Biosciences CODEX system at the HubMAP Tissue Mapping Center at the University of Florida, TMC-UF.This protocol is an overview of the CODEX raw data acquisition process guided by the CODEX Instrument Manager (CIM) , which is part of the CODEX Software Suite. The CODEX Instrument Manager is necessary to perform CODEX experiments. It controls the fluidics of the CODEX instrument the integration and synchronization with the Keyence microscope, image data formatting and facilitates transfer of data to the analysis computer.For more information, consult the Akoya Biosciences CODEX User Manual - A.0. | University of Florida, University of Florida, University of Florida, University of Florida | 1 | 2020 | Franchesca Farris, Marda Jorgensen, Jerelyn Nick, Jesus Peñaloza 2020. CODEX Acquisition Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bdifi4bn | 2021-04-15 09:15:56 | |||
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DAB Staining of FFPE Slides Resource Report Resource Website |
Jerelyn Nick, Franchesca Farris, Marda Jorgensen | DOI:10.17504/protocols.io.bdiei4be | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Standard IHC staining, such as this DAB protocol, is included in the validation of new antibodies at the University of Florida Tissue Mapping Center, TMC-Florida/Zurich. This procedure includes all of the reagents necessary to perform a DAB based immunohistochemistry reaction. DAB Substrate (3,3’-diaminobenzidine) produces a brown reaction product in the presence of peroxidase (HRP) enzyme. | University of Florida, University of Florida, University of Florida | 1 | 2020 | Jerelyn Nick, Franchesca Farris, Marda Jorgensen 2020. DAB Staining of FFPE Slides. protocols.io https://dx.doi.org/10.17504/protocols.io.bdiei4be | 2021-04-15 09:16:01 | |||
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Imaging - Stanford TMC Resource Report Resource Website |
John Hickey | DOI:10.17504/protocols.io.be8qjhvw | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | See our detailed protocol published with the following title: CODEX multiplexed tissue imaging with DNA-conjugated antibodies. | Stanford University | 1 | 2021 | John Hickey 2021. Imaging - Stanford TMC. protocols.io https://dx.doi.org/10.17504/protocols.io.be8qjhvw | 2021-04-15 09:16:07 | |||
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HuBMAP UF TMC - Single Cell RNA Seq (10x Genomics) Library Preparation and Sequencing Resource Report Resource Website |
Franchesca Farris, Maigan Brusko | DOI:10.17504/protocols.io.bffvjjn6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This protocol is for the generation of 3' (chemistry version 3) cDNA libraries from individual cells via droplet generation utilizing the 10x Genomics Chromium Controller and associated reagents. Paired end libraries are then sequenced on Illumina instruments. | University of Florida, University of Florida | 1 | 2020 | Franchesca Farris, Maigan Brusko 2020. HuBMAP UF TMC - Single Cell RNA Seq (10x Genomics) Library Preparation and Sequencing . protocols.io https://dx.doi.org/10.17504/protocols.io.bffvjjn6 | 2021-04-15 09:16:08 | |||
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HuBMAP TMC-Florida/Zurich CODEX Modality Overview Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick, Franchesca Farris, Jesus Penaloza | DOI:10.17504/protocols.io.bdcbi2sn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This protocol is an overview of all of the protocols currently in use for the CODEX modality at HubMAP Tissue Mapping Center,TMC-Florida/Zurich. It includes protocols.io links to each of the individual protocols that make up this project workflow, from processing tissue and imaging the samples, to uploading the final data to the HuBMAP HIVE. | University of Florida, University of Florida, University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Jerelyn Nick, Franchesca Farris, Jesus Penaloza 2020. HuBMAP TMC-Florida/Zurich CODEX Modality Overview. protocols.io https://dx.doi.org/10.17504/protocols.io.bdcbi2sn | 2021-04-15 09:16:10 | |||
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Multiplex Immunofluorescence on Fresh Frozen Tissue Resource Report Resource Website |
Maya Brewer, Yuantee Zhu, Elizabeth Neumann, Danielle Gutierrez, Jeff Spraggins, Mark De Caestecker | DOI:10.17504/protocols.io.665hhg6 | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:To describe the procedure for multiple cycles of immunofluorescence on human kidney tissue embedded in carboxymethylcellulose.Expected Outcome:Kidney tissue sections that have been tagged with antibodies for imaging microscopy. | Vanderbilt University Medical Center, Vanderbilt University Medical Center, Vanderbilt University, Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center | 1 | 2019 | Maya Brewer, Yuantee Zhu, Elizabeth Neumann, Danielle Gutierrez, Jeff Spraggins, Mark De Caestecker 2019. Multiplex Immunofluorescence on Fresh Frozen Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.665hhg6 | 2021-04-15 09:16:11 | |||
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Appendix for Spleen SOP Resource Report Resource Website |
Franchesca Farris | DOI:10.17504/protocols.io.bbcwiixe | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This is an appendix for spleen SOP. | University of Florida | 1 | 2020 | Franchesca Farris 2020. Appendix for Spleen SOP. protocols.io https://dx.doi.org/10.17504/protocols.io.bbcwiixe | 2021-04-15 09:16:13 | |||
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HuBMAP Tissue Sectioning for FFPE Specimens Resource Report Resource Website |
Leigh Propper, Marda Jorgensen | DOI:10.17504/protocols.io.bahdib26 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This method details our microtomy (sectioning) process for reasearch specimens involved with HuBMAP.This process follows the microtomy process that follows after receiving, processing, and embedding of research specimens into formalin fixed, paraffin embedded tissue blocks. | University of Florida, University of Florida | 2 | 2019 | Leigh Propper, Marda Jorgensen 2019. HuBMAP Tissue Sectioning for FFPE Specimens. protocols.io https://dx.doi.org/10.17504/protocols.io.bahdib26 | 2021-04-15 09:16:12 | |||
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HuBMAP: Paraffin Embedding Tissue Samples Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick | DOI:10.17504/protocols.io.bam9ic96 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the paraffin embedding of HuBMAP specimens. | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Jerelyn Nick 2020. HuBMAP: Paraffin Embedding Tissue Samples . protocols.io https://dx.doi.org/10.17504/protocols.io.bam9ic96 | 2021-04-15 09:16:24 | |||
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3D Immunostaining for CLARITY-processed samples Resource Report Resource Website |
Seth Currlin | DOI:10.17504/protocols.io.bnzdmf26 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This is a guide for immunostaining CLARITY-processed samples. dx.doi.org/10.17504/protocols.io.8jihukeThese steps are meant to be a guide for immunostaining large samples and should be optimized to suit your particular tissues and reagents. Large tissue volumes and dense tissue types will require longer incubation and wash times. The parameters suggested below are for a piece of human thymus tissue approximately 5 mm3 in size.A useful link: http://wiki.claritytechniques.org/index.php/Immunostaining | University of Florida | 1 | 2020 | Seth Currlin 2020. 3D Immunostaining for CLARITY-processed samples. protocols.io https://dx.doi.org/10.17504/protocols.io.bnzdmf26 | 2021-04-15 09:16:17 | |||
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HuBMAP Donor and Tissue Eligibility Criteria Form v 1.0 Resource Report Resource Website |
Yiing Lin, Shin Lin | DOI:10.17504/protocols.io.bqmamu2e | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Washington University, St. Louis, University of Washington | 1 | 2020 | Yiing Lin, Shin Lin 2020. HuBMAP Donor and Tissue Eligibility Criteria Form v 1.0. protocols.io https://dx.doi.org/10.17504/protocols.io.bqmamu2e | 2021-04-15 09:16:23 | ||||
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Case Processing SOP for Thymus Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick | DOI:10.17504/protocols.io.bbgmiju6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The purpose of this Standard Operating Procedure (SOP) is to outline the procedures for processing and storing thymus tissue received for HuBMAP consortium assay and analysis. | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Jerelyn Nick 2020. Case Processing SOP for Thymus . protocols.io https://dx.doi.org/10.17504/protocols.io.bbgmiju6 | 2021-04-15 09:16:47 | |||
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Imaging Mass Cytometry Modality Overview Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | DOI:10.17504/protocols.io.bgatjsen | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Unversity of Zurich, University of Florida | 2 | 2020 | Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Modality Overview . protocols.io https://dx.doi.org/10.17504/protocols.io.bgatjsen | 2021-04-15 09:16:24 |
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