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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 | 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 dx.doi.org/10.17504/protocols.io.bpyxmpxn | 2021-03-29 03:10:35 | |||
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Large Volume Immunostaining for Cleared Samples Resource Report Resource Website |
Seth Currlin, Marda Jorgensen, Jerelyn Nick | 10.17504/protocols.io.bprtmm6n | Optical Clearing of Tissue, 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 tissue (thymus, spleen, or lymph node) approximately 5 mm3 in size.A useful link: http://wiki.claritytechniques.org/index.php/Immunostaining | University of Florida, University of Florida, University of Florida | 1 | 2020 | Seth Currlin, Marda Jorgensen, Jerelyn Nick 2020. Large Volume Immunostaining for Cleared Samples. protocols.io dx.doi.org/10.17504/protocols.io.bprtmm6n | 2021-03-29 03:10:56 | |||
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Tissue Preparation for CLARITY Resource Report Resource Website |
Seth Currlin, Marda Jorgensen, Jerelyn Nick | 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 dx.doi.org/10.17504/protocols.io.8jihuke | 2021-03-29 03:11:13 | ||
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HuBMAP | Sectioning of FFPE Specimens Resource Report Resource Website |
Kelley Knizner, Christopher Simmons | 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 dx.doi.org/10.17504/protocols.io.bqqbmvsn | 2021-03-29 03:11:13 | |||
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Appendix for Spleen SOP Resource Report Resource Website |
Franchesca Farris | 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 dx.doi.org/10.17504/protocols.io.bbcwiixe | 2021-03-29 03:09:29 | |||
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Tissue Freezing for seqFISH Resource Report Resource Website |
Nina Dar, Long Cai | 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 dx.doi.org/10.17504/protocols.io.7mdhk26 | 2021-03-29 03:09:39 | |||
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HuBMAP | Formalin Fixation and Paraffin Embedding of Tissue Samples Resource Report Resource Website |
Kelley Knizner, Christopher Simmons | 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 dx.doi.org/10.17504/protocols.io.bqp6mvre | 2021-03-29 03:09:47 | |||
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Imaging Mass Cytometry Modality Overview Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | 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 dx.doi.org/10.17504/protocols.io.bgatjsen | 2021-03-29 03:10:27 | ||||
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CODEX Acquisition Protocol Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen, Jerelyn Nick, Jesus Peñaloza | 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 dx.doi.org/10.17504/protocols.io.bdifi4bn | 2021-03-29 03:08:43 | |||
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602.2 Donor Acceptance Criteria for URMC HTC HuBMAP and LungMAP Inclusion Resource Report Resource Website |
Gloria Pryhuber | 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 dx.doi.org/10.17504/protocols.io.bjuxknxn | 2021-03-29 03:08:32 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.7gehjte | 2021-03-29 03:08:31 | |||
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Cell DIVE™ Platform | Antibody Purification Chemistry Resource Report Resource Website |
Anup Sood, Eric Williams, Liz McDonough | 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 dx.doi.org/10.17504/protocols.io.bpx9mpr6 | 2021-03-29 03:08:40 | |||
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Imaging - Stanford TMC Resource Report Resource Website |
John Hickey | 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 dx.doi.org/10.17504/protocols.io.be8qjhvw | 2021-03-29 03:09:05 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.bffvjjn6 | 2021-03-29 03:09:01 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.665hhg6 | 2021-03-29 03:09:20 | |||
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Lipid Annotation of MALDI IMS Datasets Resource Report Resource Website |
Elizabeth Neumann, Jamie Allen, Jeff Spraggins, Danielle Gutierrez | 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 dx.doi.org/10.17504/protocols.io.864hzgw | 2021-03-29 03:11:53 | |||
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HuBMAP - Tissue Sectioning for CODEX Specimens Resource Report Resource Website |
Leigh Propper, Marda Jorgensen | 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 dx.doi.org/10.17504/protocols.io.basdiea6 | 2021-03-29 03:11:57 | |||
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CODEX Antibody Staining Protocol for FFPE tissues Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick | 10.17504/protocols.io.bbsdina6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This protocol describes the method for antibody staining of FFPE tissues on coverslips using CODEX Barcoded Antibodies. Included are the stepwise protocols for pre-staining, deparaffinization, antigen retrival, antibody staining and post-fixation. The enitre process requires approximately 6.5 hours, including a 3 hour incubation. Except as noted, reagents and consumables should be prepared before being the protocol. Stained tissues can be stored in CODEX Storage Buffer at 4º C for up to 2 weeks for use in CODEX multiplex imaging. | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Jerelyn Nick 2020. CODEX Antibody Staining Protocol for FFPE tissues. protocols.io dx.doi.org/10.17504/protocols.io.bbsdina6 | 2021-03-29 03:07:49 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.bjtnknme | 2021-03-29 03:08:16 | |||
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Tissue Clearing Using CLARITY Method Resource Report Resource Website |
Seth Currlin, Marda Jorgensen, Jerelyn Nick | 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 dx.doi.org/10.17504/protocols.io.bppimmke | 2021-03-29 03:08:25 |
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