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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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HubMap UF TMC Tissue Dissociation to Single Cell Resource Report Resource Website |
Marda Jorgensen, Maigan Brusko | DOI: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 https://dx.doi.org/10.17504/protocols.io.bd9vi966 | 2021-04-15 09:15:16 | ||||
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Cell DIVE™ Platform | Antibody Staining & Imaging Resource Report Resource Website |
Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood | DOI: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 https://dx.doi.org/10.17504/protocols.io.bpv6mn9e | 2021-04-15 09:15:15 | |||
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Poly-Lysine Coverslip Preparation Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen | DOI:10.17504/protocols.io.8kthuwn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Poly-Lysine Coverslip Preparation This section describes the process of creating Poly-lysine-coated coverslips that are used for the tissue slices in the CODEX® experiment workflow. | University of Florida, University of Florida | 1 | 2019 | Franchesca Farris, Marda Jorgensen 2019. Poly-Lysine Coverslip Preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.8kthuwn | 2021-04-15 09:15:43 | |||
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Case Processing SOP (Spleen) Resource Report Resource Website |
Marda Jorgensen | DOI:10.17504/protocols.io.bbcuiiww | 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 | 2 | 2020 | Marda Jorgensen 2020. Case Processing SOP (Spleen). protocols.io https://dx.doi.org/10.17504/protocols.io.bbcuiiww | 2021-04-15 09:15:21 | |||
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Isolation of single nuclei from solid tissues Resource Report Resource Website |
Blue Lake, Kun Zhang | DOI:10.17504/protocols.io.ufketkw | Human Cell Atlas Method Development Community, KPMP, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Nuclei can be readily isolated from frozen tissues with a combination of chemical and physical treatments that can circumvent the non-uniform or incomplete dissociation of solid tissues into single cells. The isolation of nuclei can also circumvent RNA degradation or any introduction of technical artefacts (such as stress responses) that could be triggered during whole cell dissociation methods. Data generated from single-nucleus genomic assays permits discovery of molecular cell types that can be used to define the overall cellular makeup of a tissue or organ, and ultimately will inform upon adult human tissue atlases. | University of California, San Diego, University of California, San Diego | http://genome-tech.ucsd.edu/ZhangLab/ | 1 | 2019 | Blue Lake, Kun Zhang 2019. Isolation of single nuclei from solid tissues. protocols.io https://dx.doi.org/10.17504/protocols.io.ufketkw | 2021-04-15 09:15:20 | ||
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HuBMAP | GE/UPitt Cell DIVE™ Modality Overview Resource Report Resource Website |
Liz McDonough | DOI:10.17504/protocols.io.bqjimuke | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | This is an overview of all protocols currently in use for the GE/UPitt Cell DIVE collaboration for the Human BioMolecular Atlas Program (HuBMAP). It includes links to each of the individual protocols that make up this project workflow. | GE Research | 1 | 2021 | Liz McDonough 2021. HuBMAP | GE/UPitt Cell DIVE™ Modality Overview. protocols.io https://dx.doi.org/10.17504/protocols.io.bqjimuke | 2021-04-15 09:15:51 | |||
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615.1 URMC HTC Non-Inflated Fresh-Frozen Embedded Lung and Associated Tissue Resource Report Resource Website |
Gloria Pryhuber, Heidie Huyck, Lisa Rogers, Cory Poole | DOI:10.17504/protocols.io.bjtnknme | Human Cell Atlas Method Development Community, Human BioMolecular Atlas Program (HuBMAP) Method Development Community, LungMap2 Consortium, URMC Pryhuber Lab | Purpose and Scope of the Procedure- Rapid blocking, embedding and freezing of human lung tissue in no freezing media, 100% OCT or 5% CMC - Rapid freezing of non-lung tissue in no freezing media, 100% OCT or 5% CMC | University of Rochester Medical Center, University of Rochester, University of Rochester Medical Center, University of Rochester | 1 | 2020 | Gloria Pryhuber, Heidie Huyck, Lisa Rogers, Cory Poole 2020. 615.1 URMC HTC Non-Inflated Fresh-Frozen Embedded Lung and Associated Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bjtnknme | 2021-04-15 09:15:34 | |||
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Tissue Clearing Using CLARITY Method Resource Report Resource Website |
Seth Currlin, Marda Jorgensen, Jerelyn Nick | DOI:10.17504/protocols.io.bppimmke | Optical Clearing of Tissue, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This document covers the CLARITY protocol for volumetric tissue clearing. This method can be applied to many tissue types and is easily modified. The link below is very useful and should be reviewed before beginning any CLARITY process. http://wiki.claritytechniques.org/index.php/CLARITY_Technique | University of Florida, University of Florida, University of Florida | 1 | 2020 | Seth Currlin, Marda Jorgensen, Jerelyn Nick 2020. Tissue Clearing Using CLARITY Method. protocols.io https://dx.doi.org/10.17504/protocols.io.bppimmke | 2021-04-15 09:15:39 | |||
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602.2 Donor Acceptance Criteria for URMC HTC HuBMAP and LungMAP Inclusion Resource Report Resource Website |
Gloria Pryhuber | DOI:10.17504/protocols.io.bjuxknxn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, LungMap2 Consortium, URMC Pryhuber Lab | Purpose and Scope of the ProcedureStandardize process for receiving lung donations Scope: Coordination of screening, acceptance and receipt of tissue for research programsPrinciples Lung donations rejected for transplantation can be used to understand human lung structure and development, ultimately to improve care of patients with lung diseaseRapid, standardized and safe processing of human tissue for the HTC requires coordination of a team of staff, materials and attention to protocolsRapid processing is required to maintain the tissues in a state as close to normal as possibleUltra-high resolution CT Scan in an inflated state will provide a high-level comparative assessment of human lung structure across developmental ages (See Protocol 603)Principles Lung donations rejected for transplantation can be used to understand human lung structure and development, ultimately to improve care of patients with lung diseaseRapid, standardized and safe processing of human tissue for the HTC requires coordination of a team of staff, materials and attention to protocolsRapid processing is required to maintain the tissues in a state as close to normal as possibleUltra-high resolution CT Scan in an inflated state will provide a high-level comparative assessment of human lung structure across developmental ages (See Protocol 603) | University of Rochester Medical Center | 1 | 2020 | Gloria Pryhuber 2020. 602.2 Donor Acceptance Criteria for URMC HTC HuBMAP and LungMAP Inclusion. protocols.io https://dx.doi.org/10.17504/protocols.io.bjuxknxn | 2021-04-15 09:15:55 | |||
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Cell DIVE™ Platform | Antibody Purification Chemistry Resource Report Resource Website |
Anup Sood, Eric Williams, Liz McDonough | DOI:10.17504/protocols.io.bpx9mpr6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | The purpose of the protocol is to purify antibodies that will be conjugated to Cy dyes as per the Cell DIVE™ technology. Affinity chromatography will be used to remove impurities from the vendor antibody to enable conjugation. | GE Research, GE Research, GE Research | 1 | 2021 | Anup Sood, Eric Williams, Liz McDonough 2021. Cell DIVE™ Platform | Antibody Purification Chemistry. protocols.io https://dx.doi.org/10.17504/protocols.io.bpx9mpr6 | 2021-04-15 09:15:53 | |||
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Protocol for Freezing in OCT Resource Report Resource Website |
Shin Lin, Yiing Lin | DOI:10.17504/protocols.io.bpx7mprn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | University of Washington, Washington University, Saint Louis | 1 | 2020 | Shin Lin, Yiing Lin 2020. Protocol for Freezing in OCT. protocols.io https://dx.doi.org/10.17504/protocols.io.bpx7mprn | 2021-04-15 09:16:02 | ||||
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Autofluorescence Microscopy Data Acquisition Resource Report Resource Website |
Elizabeth Neumann, Heath Patterson, Jamie Allen, Maya Brewer, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins | DOI:10.17504/protocols.io.7e3hjgn | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:Obtain autofluorescence microscopy images of tissues.Expected Outcome:An RGB autofluorescence microscopy image of the tissue section that enables registration and correlation of different imaging modalities on a pixel by pixel basis. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center, Vanderbilt University, Vanderbilt University | 1 | 2019 | Elizabeth Neumann, Heath Patterson, Jamie Allen, Maya Brewer, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins 2019. Autofluorescence Microscopy Data Acquisition. protocols.io https://dx.doi.org/10.17504/protocols.io.7e3hjgn | 2021-04-15 09:16:02 | |||
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Freezing Fresh Tissue Resource Report Resource Website |
Jeff Spraggins, Elizabeth Neumann, Mark deCaestecker, Danielle Gutierrez, Jamie Allen, Maya Brewer | DOI:10.17504/protocols.io.4smgwc6 | 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 Medical Center, Vanderbilt University, Vanderbilt University, Vanderbilt University | 1 | 2019 | Jeff Spraggins, Elizabeth Neumann, Mark deCaestecker, Danielle Gutierrez, Jamie Allen, Maya Brewer 2019. Freezing Fresh Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.4smgwc6 | 2021-04-15 09:16:13 | |||
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HuBMAP UF TMC - 10x Genomics scRNAseq Modality Overview Resource Report Resource Website |
Marda Jorgensen, Maigan Brusko | DOI:10.17504/protocols.io.be79jhr6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Maigan Brusko 2020. HuBMAP UF TMC - 10x Genomics scRNAseq Modality Overview . protocols.io https://dx.doi.org/10.17504/protocols.io.be79jhr6 | 2021-04-15 09:16:19 | ||||
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Tissue Freezing for seqFISH Resource Report Resource Website |
Nina Dar, Long Cai | DOI:10.17504/protocols.io.7mdhk26 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Once a tissue is received, it should be frozen using the following protocol: | California Institute of Technology, California Institute of Technology | 1 | 2019 | Nina Dar, Long Cai 2019. Tissue Freezing for seqFISH. protocols.io https://dx.doi.org/10.17504/protocols.io.7mdhk26 | 2021-04-15 09:16:15 | |||
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HuBMAP | Formalin Fixation and Paraffin Embedding of Tissue Samples Resource Report Resource Website |
Kelley Knizner, Christopher Simmons | DOI:10.17504/protocols.io.bqp6mvre | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | This method details formalin fixation and paraffin embedding of the HuBMAP tissue specimens.Protocol adopted from Marda Jorgensen, Jerelyn Nick (02/24/2020). HuBMAP: Paraffin Embedding Tissue Samples . https://dx.doi.org/10.17504/protocols.io.bam9ic96 | University of Pittsburgh Medical Center, University of Pittsburgh Medical Center | 1 | 2020 | Kelley Knizner, Christopher Simmons 2020. HuBMAP | Formalin Fixation and Paraffin Embedding of Tissue Samples . protocols.io https://dx.doi.org/10.17504/protocols.io.bqp6mvre | 2021-04-15 09:16:16 | |||
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Antibody Purification and Labeling Resource Report Resource Website |
Maya Brewer, Yuantee Zhu, Danielle Gutierrez, Jeff Spraggins, Mark De Caestecker | DOI:10.17504/protocols.io.667hhhn | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This protocol describes the process for antibody purification and subsequent labeling for direct immunofluorescence. | Vanderbilt University, Vanderbilt University Medical Center, Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center | 1 | 2019 | Maya Brewer, Yuantee Zhu, Danielle Gutierrez, Jeff Spraggins, Mark De Caestecker 2019. Antibody Purification and Labeling. protocols.io https://dx.doi.org/10.17504/protocols.io.667hhhn | 2021-04-15 09:16:17 | |||
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Imaging Mass Cytometry Data Acquisition Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | DOI:10.17504/protocols.io.bf2ijqce | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This SOP describes the image acquisition with an Imaging Mass Cytometer (IMC orHyperion).Prior to this protocol the IMC needs to be fully tuned to specifications (see“HuBMAP_Protocol_4_IMC_Tuning.pdf”). Additionally, every batch of samples stainedwith the same antibody-mix requires the acquisition of a compensation slide for spill overcorrection (see “HuBMAP_Protocol_3_Compensation_Slide_Preparation.pdf” &“HuBMAP_Protocol_6_IMC_Compensation_Slide_Acquisition.pdf”). | University of Zürich, University of Florida | 1 | 2020 | Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Data Acquisition. protocols.io https://dx.doi.org/10.17504/protocols.io.bf2ijqce | 2021-04-15 09:16:25 | |||
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CODEX Microtomy Tracking Sheet Resource Report Resource Website |
Leigh Propper, Marda Jorgensen | DOI:10.17504/protocols.io.baefibbn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Microtomy Tracking Sheet for CODEX SpecimensThe process of sectioning CODEX specimens presents tediously at the tissue block trimming and microtomy stage.As you begin to cut into a new or already used tissue block, you must keep track of how many microns of tissue are removed from the section during trimming, and also during microtomy.Attached is a generic document that is used to keep record of what tissue block is being cut. All identification factors, trimming data, what tissue sections were used and their purpose, as well as storage information. Formal logging of how far into the tissue block you have traveled as well as how many sections were used is an extremely important and necessary function in this process. | University of Florida, University of Florida | 1 | 2019 | Leigh Propper, Marda Jorgensen 2019. CODEX Microtomy Tracking Sheet. protocols.io https://dx.doi.org/10.17504/protocols.io.baefibbn | 2021-04-15 09:16:22 | |||
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Cutting FFPE Sections for Imaging Mass Cytometry Resource Report Resource Website |
Marda Jorgensen, Michelle Daniel | DOI:10.17504/protocols.io.bfz4jp8w | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | FFPE block are cut into thin sections. | University of Florida, University of Zürich | 1 | 2020 | Marda Jorgensen, Michelle Daniel 2020. Cutting FFPE Sections for Imaging Mass Cytometry. protocols.io https://dx.doi.org/10.17504/protocols.io.bfz4jp8w | 2021-04-15 09:16:43 |
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