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| Name | Authors | DOI | Group |
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Associated Publications |
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Shipping Paraffin Blocks to the Bodenmiller Lab for IMC Analysis Resource Report Resource Website |
Marda Jorgensen | 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 dx.doi.org/10.17504/protocols.io.bf5njq5e | 2021-03-29 03:12:26 | |||
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10X Genomics Single-Nucleus RNA-Sequencing for Transcriptomic Profiling of Adult Human Tissues Resource Report Resource Website |
Sarah Urata, Blue Lake, Dinh Diep, Masato Hoshi, Sanjay Jain, Kun Zhang | 10.17504/protocols.io.86khzcw | KPMP, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | 10X Genomics Single Cell 3' (v3) RNA sequencing is a microdroplet-based method that permits the effective capture and sequencing of the mRNA and pre-mRNA molecules from single nuclei [1]. RNA molecules are transcribed and processed within the nucleus before exporting to ER for translation into proteins. As such, nuclear RNA is a mixture of nascent transcripts, partially or fully processed mRNA, and various non-coding RNA molecules. The total RNA content within the nucleus is roughly 10% of the RNA content in a whole cell, but has been found to accurately represent whole cell expression values in adult human tissues [2,3] including the kidney [4]. Nuclei can be readily isolated from frozen tissues with a combination of chemical and physical treatments that can effectively circumvent the non-uniform or incomplete dissociation of solid tissues into single cells, as well as RNA degradation or artefacts (such as stress response) during dissociation. Here we present a modified version of the published 10X protocol [1] that we have adapted for the processing of adult human kidney nuclei.References 1. Chromium Single Cell 3' Reagent Kits v3 User Guide (Rev A) CG000183, support.10xgenomics.com. 2. Lake et al. (2016). Science, doi:10.1126/science.aaf1204. 3. Lake et al. (2018). Nature Biotechnology, doi:10.1038/nbt.4038. 4. Lake et al. (2019). Nature Communications, doi:10.1038/s41467-019-10861-2. | University of California, San Diego, University of California, San Diego, University of California, San Diego, Washington University, Saint Louis, Washington University School of Medicine, Saint Louis, University of California, San Diego | http://genome-tech.ucsd.edu/ZhangLab/ | 3 | 2019 | Sarah Urata, Blue Lake, Dinh Diep, Masato Hoshi, Sanjay Jain, Kun Zhang 2019. 10X Genomics Single-Nucleus RNA-Sequencing for Transcriptomic Profiling of Adult Human Tissues. protocols.io dx.doi.org/10.17504/protocols.io.86khzcw | 2021-03-29 03:12:28 | ||
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Reagent prep - Stanford TMC Resource Report Resource Website |
John Hickey | 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 dx.doi.org/10.17504/protocols.io.be92jh8e | 2021-03-29 03:12:30 | |||
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VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN) Resource Report Resource Website |
Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins | 10.17504/protocols.io.bb2wiqfe | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | We aim to develop high resolution, chemically informative imaginig methodologies for building an atlas of human organs, such as the kidney.Scope:Provide an overview of the methods used by the Vanderbilt Tissue Mapping Center as part of the Human Biomolecular Atlas Program (HuBMAP, NIH Common Fund) and contextualize individual protocols within our larger workflow. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center, Vanderbilt University, Vanderbilt University | 2 | 2020 | Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins 2020. VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN). protocols.io dx.doi.org/10.17504/protocols.io.bb2wiqfe | 2021-03-29 03:12:34 | |||
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LC-MS/MS Label-Free Proteomic Data Analysis Parameters Resource Report Resource Website |
Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins | 10.17504/protocols.io.bfshjnb6 | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | List of parameters and settings for searching label free proteomic data in MaxQuant version 1.6.7. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 2 | 2020 | Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins 2020. LC-MS/MS Label-Free Proteomic Data Analysis Parameters. protocols.io dx.doi.org/10.17504/protocols.io.bfshjnb6 | 2021-03-29 03:12:37 | |||
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SOP Appendix for Spleen Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen | 10.17504/protocols.io.bcwhixb6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This is an appendix for spleen SOP. | University of Florida, University of Florida | 2 | 2020 | Franchesca Farris, Marda Jorgensen 2020. SOP Appendix for Spleen. protocols.io dx.doi.org/10.17504/protocols.io.bcwhixb6 | 2021-03-29 03:12:36 | |||
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Cell DIVE™ Platform | Slide Clearing and Antigen Retrieval Resource Report Resource Website |
Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood | 10.17504/protocols.io.bpwumpew | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | The purpose of this protocol is to manually deparaffinize and rehydrate slides for the Cell DIVE™ Platform. | 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 | Slide Clearing and Antigen Retrieval. protocols.io dx.doi.org/10.17504/protocols.io.bpwumpew | 2021-03-29 03:12:38 | |||
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HuBMAP UF TMC - FACS Sorting of Live Cells for 10x scRNASeq Resource Report Resource Website |
Maigan Brusko | 10.17504/protocols.io.bfqzjmx6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This standard operating procedure (SOP) provides instructions for staining and sorting live cells. This SOP applies to cryopreserved cells that are stained with Live/Dead and sorted in the BD ARIA III to remove dead cells prior to 10x sequencing. | University of Florida | 1 | 2020 | Maigan Brusko 2020. HuBMAP UF TMC - FACS Sorting of Live Cells for 10x scRNASeq. protocols.io dx.doi.org/10.17504/protocols.io.bfqzjmx6 | 2021-03-29 03:12:42 | |||
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Storage and Processing of Tissue for bulk RNA Isolation Resource Report Resource Website |
Aaron Horning | 10.17504/protocols.io.bf52jq8e | NCIHTAN, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Stanford University | 1 | 2020 | Aaron Horning 2020. Storage and Processing of Tissue for bulk RNA Isolation. protocols.io dx.doi.org/10.17504/protocols.io.bf52jq8e | 2021-03-29 03:12:51 | ||||
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Maxpar Antibody Labeling for Imaging Mass Cytometry Resource Report Resource Website |
Marda Jorgensen, Michelle Daniel | 10.17504/protocols.io.bf5jjq4n | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Version 11 of the antibody labelling protocol published by Fluidigm. | University of Florida, University of Zürich | 1 | 2020 | Marda Jorgensen, Michelle Daniel 2020. Maxpar Antibody Labeling for Imaging Mass Cytometry. protocols.io dx.doi.org/10.17504/protocols.io.bf5jjq4n | 2021-03-29 03:13:06 | |||
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LC-MS/MS Label-Free Proteomic Data Acquisition Resource Report Resource Website |
Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins | 10.17504/protocols.io.bs7hnhj6 | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Description of settings used to acquire LC-MS/MS data from label-free proteomic samples. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 4 | 2021 | Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins 2021. LC-MS/MS Label-Free Proteomic Data Acquisition. protocols.io dx.doi.org/10.17504/protocols.io.bs7hnhj6 | 2021-03-29 03:13:06 | |||
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RNA Extraction for RIN and DV 200 Analysis Resource Report Resource Website |
Jamie Allen, Elizabeth Neumann, Maya Brewer, Jeff Spraggins, Danielle Gutierrez, Mark De Caestecker | 10.17504/protocols.io.86nhzde | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope: Extract RNA for RIN and DV 200 Assessment.Expected Outcome: RIN and DV 200 measurements for tissue quality assessment. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center | 1 | 2020 | Jamie Allen, Elizabeth Neumann, Maya Brewer, Jeff Spraggins, Danielle Gutierrez, Mark De Caestecker 2020. RNA Extraction for RIN and DV 200 Analysis. protocols.io dx.doi.org/10.17504/protocols.io.86nhzde | 2021-03-29 03:13:08 | |||
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VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN) Resource Report Resource Website |
Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins | 10.17504/protocols.io.beevjbe6 | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | We aim to develop high resolution, chemically informative imaginig methodologies for building an atlas of human organs, such as the kidney.Scope:Provide an overview of the methods used by the Vanderbilt Tissue Mapping Center as part of the Human Biomolecular Atlas Program (HuBMAP, NIH Common Fund) and contextualize individual protocols within our larger workflow. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center, Vanderbilt University, Vanderbilt University | 3 | 2020 | Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins 2020. VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN). protocols.io dx.doi.org/10.17504/protocols.io.beevjbe6 | 2021-03-29 03:13:12 | |||
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Cryostat Sectioning of Tissues for 3D Multimodal Molecular Imaging Resource Report Resource Website |
David Anderson, Elizabeth Neumann, Jamie Allen, Maya Brewer, Danielle Gutierrez, Jeff Spraggins | 10.17504/protocols.io.7ethjen | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope: Protocol for sectioning flash frozen tissue that can be used for 3D IMS or MxIF experiments.Expected Outcome:Serial sections from a tissue that IMS and MxIF can be performed on with subsequent 3D reconstruction | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 1 | 2019 | David Anderson, Elizabeth Neumann, Jamie Allen, Maya Brewer, Danielle Gutierrez, Jeff Spraggins 2019. Cryostat Sectioning of Tissues for 3D Multimodal Molecular Imaging. protocols.io dx.doi.org/10.17504/protocols.io.7ethjen | 2021-03-29 03:13:30 | |||
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Lightsheet Microscope Acquisition Protocol Resource Report Resource Website |
Marda Jorgensen, Seth Currlin | 10.17504/protocols.io.begajbse | 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 lightsheet 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 lightsheet 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 lightsheet 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 lasersheet 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 lightsheet alignment | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Seth Currlin 2020. Lightsheet Microscope Acquisition Protocol. protocols.io dx.doi.org/10.17504/protocols.io.begajbse | 2021-03-29 03:13:42 | |||
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HuBMAP TMC-Florida/Zurich Light Sheet Fluorescence Microscopy Modality Overview Resource Report Resource Website |
Jerelyn Nick, Marda Jorgensen, Seth Currlin | 10.17504/protocols.io.bqaamsae | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This protocol is an overview of all of the protocols currently in use for the Light Sheet Fluorescence Microscopy 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 | 1 | 2020 | Jerelyn Nick, Marda Jorgensen, Seth Currlin 2020. HuBMAP TMC-Florida/Zurich Light Sheet Fluorescence Microscopy Modality Overview. protocols.io dx.doi.org/10.17504/protocols.io.bqaamsae | 2021-03-29 03:13:46 | |||
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Human Kidney, Urinary Tract, and Lung Cell Type Mapping Pipeline for the Human Biomolecular Atlas Program (HuBMAP) Resource Report Resource Website |
Blue Lake, Elizabeth Duong, Dinh Diep, Xin Sun, Peter K, Jim Hagood, Gloria Pryhuber, Sanjay Jain, Kun Zhang [University Of California | 10.17504/protocols.io.bj9wkr7e | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This document provides an overview of the protocols used by the Human Kidney, Urinary Tract, and Lung Mapping Center (KULMAP) for generation of spatially resolved mulitomic cell type organ maps within HuBMAP. This involves sequencing of the transcriptomes and epigenomes of dissociated single cells in a massively parallel manner, which will then inform on a highly multiplexed RNA in situ imaging method (DART-FISH) for spatial mapping of hundreds of molecular targets in the tissue sections, at a subcellular resolution. These spatial molecular maps will serve as scaffolds for computational registration of cell types and the associated transcriptome/chromatin maps to the tissue space. | University of California, San Diego, University of California, San Diego, University of California, San Diego, University of California, San Diego, Harvard Medical School, University of North Carolina at Chapel Hill, University of Rochester Medical Center, Washington University, Saint Louis, University of California, San Diego | 1 | 2020 | Blue Lake, Elizabeth Duong, Dinh Diep, Xin Sun, Peter K, Jim Hagood, Gloria Pryhuber, Sanjay Jain, Kun Zhang [University Of California 2020. Human Kidney, Urinary Tract, and Lung Cell Type Mapping Pipeline for the Human Biomolecular Atlas Program (HuBMAP). protocols.io dx.doi.org/10.17504/protocols.io.bj9wkr7e | 2021-03-29 03:13:47 | |||
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VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN) Resource Report Resource Website |
Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins | 10.17504/protocols.io.bfskjncw | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | We aim to develop high resolution, chemically informative imaginig methodologies for building an atlas of human organs, such as the kidney.Scope:Provide an overview of the methods used by the Vanderbilt Tissue Mapping Center as part of the Human Biomolecular Atlas Program (HuBMAP, NIH Common Fund) and contextualize individual protocols within our larger workflow. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center, Vanderbilt University, Vanderbilt University | 4 | 2020 | Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins 2020. VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN). protocols.io dx.doi.org/10.17504/protocols.io.bfskjncw | 2021-03-29 03:13:56 | |||
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Donor Acceptance Criteria for GE/UPitt HuBMAP Inclusion Resource Report Resource Website |
Ho, Jonhan | 10.17504/protocols.io.bqi6muhe | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | This document outlines the required criteria for donor inclusion of skin specimens in the Human BioMolecular Atlas Program (HuBMAP). The study intends to be as inclusive as possible of race and ethnicity, dependent only on the consent for donor tissue for research. Disease known at the time of donation or later identified during the research will not necessarily exclude the sample from the research program. | University of Pittsburgh Medical Center | 1 | 2020 | Ho, Jonhan 2020. Donor Acceptance Criteria for GE/UPitt HuBMAP Inclusion. protocols.io dx.doi.org/10.17504/protocols.io.bqi6muhe | 2021-03-29 03:14:00 | |||
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Imaging Mass Cytometry Compensation Slide Preparation Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | 10.17504/protocols.io.bf2djqa6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This SOP describes the preparation of compensation slides with single antibodyconjugatespots that can be used to estimate mass channel spillover for IMC. Spillovervaries from metal lot to lot due to varying impurities. Once a spillover matrix for a specificset of antibody-conjugates has been generated, the experiment of interest, in which thesame antibody conjugates have been used, can be spillover-corrected.It is crucial that this procedure is performed for the exact same antibody conjugates thatare used to pipette the antibody panel for sample staining.The original publication can be viewed here:“Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry” by S.Chevrier, HL Crowell and VRT Zanotelli et al., Cell Systems, 2018 | University of Zürich, University of Florida | 1 | 2020 | Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Compensation Slide Preparation. protocols.io dx.doi.org/10.17504/protocols.io.bf2djqa6 | 2021-03-29 03:14:18 |
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