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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Cell DIVE™ Platform | Antibody Characterization for Multiplexing Resource Report Resource Website |
Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood | DOI:10.17504/protocols.io.bpyxmpxn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | This protocol describes the process of validating antibodies (primary/secondary, direct conjugates, and zenon labelled) as per the Cell DIVE™ technology. It also describes the process for determining any antigen effects from the dye inactivation process. | 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 Characterization for Multiplexing. protocols.io https://dx.doi.org/10.17504/protocols.io.bpyxmpxn | 2021-04-15 09:16:26 | |||
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FFPE Tissue Sectioning for Staining Resource Report Resource Website |
Marda Jorgensen | DOI:10.17504/protocols.io.8kvhuw6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Method for sectioning paraffin blocks for staining | University of Florida | 1 | 2019 | Marda Jorgensen 2019. FFPE Tissue Sectioning for Staining. protocols.io https://dx.doi.org/10.17504/protocols.io.8kvhuw6 | 2021-04-15 09:16:54 | |||
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Imaging Mass Cytometry Antibody Staining Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | DOI:10.17504/protocols.io.bfz8jp9w | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The following SOP describes procedures required for the antibody staining of formalin fixed,paraffin-embedded (FFPE) samples. In this SOP, the term “samples” refers to FFPEtissue samples. | University of Zürich, University of Florida | 1 | 2020 | Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Antibody Staining . protocols.io https://dx.doi.org/10.17504/protocols.io.bfz8jp9w | 2021-04-15 09:16:56 | |||
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Cell DIVE™ Platform | Ab Conjugation: Initial Conjugation & Scale up Conjugation Resource Report Resource Website |
Anup Sood, Eric Williams, Liz McDonough | DOI:10.17504/protocols.io.bp55mq86 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | ScopeThe purpose of this protocol is to conjugate purified antibodies to Cy dyes. Antibody conjugation involves combining dyes with antibodies to achieve a fluorescently labeled antibody. Each antibody will be labeled with a molar equivalent of dye; the quantitative output of this is deemed D/P. In the initial conjugation step, each antibody will be labeled with differing D/P levels and validated to determine which level is optimal. | GE Research, GE Research, GE Research | 1 | 2021 | Anup Sood, Eric Williams, Liz McDonough 2021. Cell DIVE™ Platform | Ab Conjugation: Initial Conjugation & Scale up Conjugation. protocols.io https://dx.doi.org/10.17504/protocols.io.bp55mq86 | 2021-04-15 09:16:29 | |||
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Automated, Rapid Preparation of Tissue Sections for Proteomic Analysis Resource Report Resource Website |
Jamie Allen, Jeff Spraggins, Danielle Gutierrez | DOI:10.17504/protocols.io.67nhhme | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:To describe the procedure for the lysis, reduction/alkylation, trypsin digestion, and clean-up of tissue. Lysis will cover the lysing of tissue and protein concentration. Acetone precipitation will cover the precipitation of proteins. Digestion will cover the process for digesting 100 µg of protein using the Agilent AssayMap Bravo Robot and Promega Rapid Trypsin/LysC. The clean-up of the cells will cover the desalting process on the Agilent AssayMap Bravo and the subsequent preparation of the samples for LC/MS peptide analysis.Expected Outcome/Data:Cell samples lysed, digested, and desalted for analysis on MS instrument. Samples to be analyzed within one or two days of desalting. | Vanderbilt University, Vanderbilt University, Vanderbilt University | https://www.thermofisher.com/order/catalog/product/23225 | 2 | 2019 | Jamie Allen, Jeff Spraggins, Danielle Gutierrez 2019. Automated, Rapid Preparation of Tissue Sections for Proteomic Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.67nhhme | 2021-04-15 09:16:35 | ||
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Imaging Mass Cytometer Tuning Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | DOI:10.17504/protocols.io.bf2gjqbw | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This SOP describes the tuning of an Imaging Mass Cytometer (IMC). The tuning processencompasses parameters such as Interface alignment, gas flow rate optimizations, laserpower optimization and detector voltage optimization. All these factors aim at having amachine that performs equally over time.The machine needs to pass specifications listed in this SOP in order to be used for dataacquisition.Machines do not need to be tuned daily but at least twice per week and upon every startup.Additionally, the adjustment of the laser energy is described in this SOP, whichneeds to be performed every 3 weeks. | University of Zurich, University of Florida | 1 | 2020 | Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometer Tuning . protocols.io https://dx.doi.org/10.17504/protocols.io.bf2gjqbw | 2021-04-15 09:16:36 | |||
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Post-IMS Autofluorescence Microscopy Resource Report Resource Website |
Elizabeth Neumann, Jamie Allen, Heath Patterson, Danielle Gutierrez, Jeff Spraggins | DOI:10.17504/protocols.io.879hzr6 | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope: Obtain autofluorescence microscopy images of tissues after IMS analysisExpected Outcome: A brightfield and green 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, Vanderbilt University | 1 | 2020 | Elizabeth Neumann, Jamie Allen, Heath Patterson, Danielle Gutierrez, Jeff Spraggins 2020. Post-IMS Autofluorescence Microscopy. protocols.io https://dx.doi.org/10.17504/protocols.io.879hzr6 | 2021-04-15 09:16:58 | |||
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HuBMAP | Sectioning of FFPE Specimens Resource Report Resource Website |
Kelley Knizner, Christopher Simmons | DOI:10.17504/protocols.io.bqqbmvsn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | This method details sectioning of the FFPE HuBMAP specimens.Protocol adopted from Leigh Propper, Marda Jorgensen (12/13/2019). HuBMAP Tissue Sectioning for FFPE Specimens. https://dx.doi.org/10.17504/protocols.io.bahdib26 | University of Pittsburgh Medical Center, University of Pittsburgh Medical Center | 1 | 2020 | Kelley Knizner, Christopher Simmons 2020. HuBMAP | Sectioning of FFPE Specimens. protocols.io https://dx.doi.org/10.17504/protocols.io.bqqbmvsn | 2021-04-15 09:16:37 | |||
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Tissue Preparation for CLARITY Resource Report Resource Website |
Seth Currlin, Marda Jorgensen, Jerelyn Nick | DOI:10.17504/protocols.io.8jihuke | Optical Clearing of Tissue, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Tissue preparation for CLARITY includes fixation in 4% PFA, infusion with monomers in Hydrogel Solution, and clearing of lipids in Electrophoretic Tissue Clearing Solution. | University of Florida, University of Florida, University of Florida | http://wiki.claritytechniques.org/index.php/Solutions | 1 | 2019 | Seth Currlin, Marda Jorgensen, Jerelyn Nick 2019. Tissue Preparation for CLARITY. protocols.io https://dx.doi.org/10.17504/protocols.io.8jihuke | 2021-04-15 09:16:37 | ||
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Initial Rapid Pathology Assessment of Kidney Tissue Resource Report Resource Website |
Jamie Allen, Elizabeth Neumann, Maya Brewer, Haichun Yang, Jeff Spraggins, Danielle Gutierrez | DOI:10.17504/protocols.io.9dph25n | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:Prepare formalin fixed tissue with freezing fresh tissue protocol (dx.doi.org/10.17504/protocols.io.6wghfbw). This protocol provides the steps to prepare formalin fixed human kidney tissue and perform histology assessment for normalcy.Expected Outcome:Pathological assessment of kidney tissue for use in LC-MS/MS and imaging. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 1 | 2020 | Jamie Allen, Elizabeth Neumann, Maya Brewer, Haichun Yang, Jeff Spraggins, Danielle Gutierrez 2020. Initial Rapid Pathology Assessment of Kidney Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.9dph25n | 2021-04-15 09:16:46 | |||
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Light Sheet Fluorescence Microscopy Image Acquisition Resource Report Resource Website |
Seth Currlin, Marda Jorgensen, Jerelyn Nick | DOI:10.17504/protocols.io.bprsmm6e | Optical Clearing of Tissue, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The Zeiss Lightsheet 7 is used to quickly and efficiently scan large tissue volumes using laser light sheet illumination. The focused laser sheets and imaging plane are static while the tissue is moved throughout the selected volume for three dimensional image acquisition. This protocol will cover the procedures used for the day of light sheet image acquisition.Setting the acquisition volume: Large scanning volumes are composed of multiple z-stack being stitched back together based on overlapping edges of the scanning window. This requires setting an overall z-stack, which must include the entirety of tissue as covered by adjoining z-stacks. This becomes tricky when considering irregularly shaped tissues and their orientation relative to the various laser and imaging objectives.Dual-side light sheet alignment: To obtain a strong and clear image from large tissues it is helpful to illuminate the sample with both the left and right laser. Each laser sheet can be angled slightly within the focal plane to account for differences in the R.I. of the tissue and R.I. media (TDE). This is a manual tuning process and is not intended for major R.I. differences.Protocol Overview:- Refractive index matching of cleared tissue samples. - Mounting tissue onto sample holder.- Image acquisition in Zen 3.1 LS (black edition), including: - Setting the acquisition volume - Dual-sided light sheet alignment | University of Florida, University of Florida, University of Florida | 1 | 2020 | Seth Currlin, Marda Jorgensen, Jerelyn Nick 2020. Light Sheet Fluorescence Microscopy Image Acquisition. protocols.io https://dx.doi.org/10.17504/protocols.io.bprsmm6e | 2021-04-15 09:16:59 | |||
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Lipid Annotation of MALDI IMS Datasets Resource Report Resource Website |
Elizabeth Neumann, Jamie Allen, Jeff Spraggins, Danielle Gutierrez | DOI:10.17504/protocols.io.864hzgw | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope: Annotate lipid species detected by MALDI IMS analysis.Expected Outcome:A list of lipid identifications with low mass errors ( | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 1 | 2020 | Elizabeth Neumann, Jamie Allen, Jeff Spraggins, Danielle Gutierrez 2020. Lipid Annotation of MALDI IMS Datasets. protocols.io https://dx.doi.org/10.17504/protocols.io.864hzgw | 2021-04-15 09:16:51 | |||
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Imaging Mass Cytometry Compensation Slide Acquisition Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | DOI:10.17504/protocols.io.bf2jjqcn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This SOP describes the slide acquisition for spill-over correction of Imaging MassCytometry experiments. The protocol makes use of the compensation slide, which wasprepared previously following the SOP:“HuBMAP_Protocol_3_Compensation_Slide_Preparation.pdf” to measure eachconjugated antibody individually and to record all observed spill-over. The resultingcompensation matrix can be used to compensate data that has been recorded using thesame antibody conjugates. | University of Zürich, Unversity of Florida | 1 | 2020 | Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Compensation Slide Acquisition. protocols.io https://dx.doi.org/10.17504/protocols.io.bf2jjqcn | 2021-04-15 09:17:03 | |||
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HuBMAP - Tissue Sectioning for CODEX Specimens Resource Report Resource Website |
Leigh Propper, Marda Jorgensen | DOI:10.17504/protocols.io.basdiea6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This method details the microtomy process for specimens that will be stained and analyzed using the Akoya CODEX® system.This process applies to paraffin embedded blocks containing tissue of no more than 1cm x 1cm in size.FFPE tissues for CODEX® analysis must be sectioned onto prepared poly-l-lysine coated coverslips.Cut and mounted tissue sections can be stored at 4°C for up to one(1 )month prior to staining. | University of Florida, University of Florida | 2 | 2019 | Leigh Propper, Marda Jorgensen 2019. HuBMAP - Tissue Sectioning for CODEX Specimens. protocols.io https://dx.doi.org/10.17504/protocols.io.basdiea6 | 2021-04-15 09:16:53 | |||
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Nano-DESI Mass Spectrometry Imaging kidney characterization pipeline for tissues collected by Vanderbilt University Resource Report Resource Website |
yang1832 , Julia Laskin | DOI:10.17504/protocols.io.bmwik7ce | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, NanoDESI MSI Julia Laskin group Purdue | Our goal is to map the biological tissues with Nano-DESI Mass Spectrometry Imaging and build an atlas of human kidney.Scope: Provide an overview of the sample preparation steps used by the Vanderbilt Tissue Mapping Center and Nano-DESI MSI workflow used by Julia Laskin's group as part of the Human Biomolecular Atlas Program (HuBMAP, NIH Common Fund). | Purdue University, Purdue University | 1 | 2020 | yang1832 , Julia Laskin 2020. Nano-DESI Mass Spectrometry Imaging kidney characterization pipeline for tissues collected by Vanderbilt University. protocols.io https://dx.doi.org/10.17504/protocols.io.bmwik7ce | 2021-04-15 09:17:08 | |||
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Sample prep - Stanford TMC Resource Report Resource Website |
John Hickey | DOI:10.17504/protocols.io.be9zjh76 | 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. Sample prep - Stanford TMC. protocols.io https://dx.doi.org/10.17504/protocols.io.be9zjh76 | 2021-04-15 09:17:04 | |||
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Freezing Fresh Tissue Resource Report Resource Website |
Jamie Allen, Maya Brewer, Elizabeth Neumann, Danielle Gutierrez, Mark deCaestecker, Jeff Spraggins | DOI: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 https://dx.doi.org/10.17504/protocols.io.6wghfbw | 2021-04-15 09:17:09 | |||
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Donor Acceptance Criteria for TMC Florida/Zurich HuBMAP Inclusion Resource Report Resource Website |
Marda Jorgensen | DOI:10.17504/protocols.io.bipykdpw | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This document outlines the required criteria for inclusion for donors of thymus, lymph nodes and spleen in the HuBMAP project. | University of Florida | 1 | 2020 | Marda Jorgensen 2020. Donor Acceptance Criteria for TMC Florida/Zurich HuBMAP Inclusion. protocols.io https://dx.doi.org/10.17504/protocols.io.bipykdpw | 2021-04-15 09:14:21 | |||
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Shipping Paraffin Blocks to the Bodenmiller Lab for IMC Analysis Resource Report Resource Website |
Marda Jorgensen | DOI:10.17504/protocols.io.bf5njq5e | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This SOP describes the methods used to ship paraffin-embedded blocks to the University of Zurich. | University of Florida | 1 | 2020 | Marda Jorgensen 2020. Shipping Paraffin Blocks to the Bodenmiller Lab for IMC Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.bf5njq5e | 2021-04-15 09:14:24 | |||
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Reagent prep - Stanford TMC Resource Report Resource Website |
John Hickey | DOI:10.17504/protocols.io.be92jh8e | 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. Reagent prep - Stanford TMC. protocols.io https://dx.doi.org/10.17504/protocols.io.be92jh8e | 2021-04-15 09:14:27 |
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