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Authors: Marda Jorgensen, Maigan Brusko
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Proper citation: Marda Jorgensen, Maigan Brusko 2020. HubMap UF TMC Tissue Dissociation to Single Cell. protocols.io https://dx.doi.org/10.17504/protocols.io.bd9vi966 Copy
Authors: Liz McDonough, Chrystal Chadwick, Fiona Ginty, Christine Surrette, Anup Sood
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research
Summary: This document outlines the workflow for antibody staining, dye inactivation, and imaging as per the Cell DIVE™ technology.
Proper citation: 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 Copy
Authors: Franchesca Farris, Marda Jorgensen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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.
Proper citation: Franchesca Farris, Marda Jorgensen 2019. Poly-Lysine Coverslip Preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.8kthuwn Copy
Authors: Marda Jorgensen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: The purpose of this Standard Operating Procedure is to outline procedures for processing and storing spleen received for HuBMAP consortium assay and analysis.
Proper citation: Marda Jorgensen 2020. Case Processing SOP (Spleen). protocols.io https://dx.doi.org/10.17504/protocols.io.bbcuiiww Copy
Authors: Blue Lake, Kun Zhang
Group: Human Cell Atlas Method Development Community, KPMP, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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.
Proper citation: Blue Lake, Kun Zhang 2019. Isolation of single nuclei from solid tissues. protocols.io https://dx.doi.org/10.17504/protocols.io.ufketkw Copy
Authors: Liz McDonough
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research
Summary: 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.
Proper citation: Liz McDonough 2021. HuBMAP | GE/UPitt Cell DIVE™ Modality Overview. protocols.io https://dx.doi.org/10.17504/protocols.io.bqjimuke Copy
Authors: Gloria Pryhuber, Heidie Huyck, Lisa Rogers, Cory Poole
Group: Human Cell Atlas Method Development Community, Human BioMolecular Atlas Program (HuBMAP) Method Development Community, LungMap2 Consortium, URMC Pryhuber Lab
Summary: 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
Proper citation: 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 Copy
Authors: Seth Currlin, Marda Jorgensen, Jerelyn Nick
Group: Optical Clearing of Tissue, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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
Proper citation: Seth Currlin, Marda Jorgensen, Jerelyn Nick 2020. Tissue Clearing Using CLARITY Method. protocols.io https://dx.doi.org/10.17504/protocols.io.bppimmke Copy
Authors: Gloria Pryhuber
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, LungMap2 Consortium, URMC Pryhuber Lab
Summary: 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)
Proper citation: 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 Copy
Authors: Anup Sood, Eric Williams, Liz McDonough
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research
Summary: 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.
Proper citation: Anup Sood, Eric Williams, Liz McDonough 2021. Cell DIVE™ Platform | Antibody Purification Chemistry. protocols.io https://dx.doi.org/10.17504/protocols.io.bpx9mpr6 Copy
Authors: Shin Lin, Yiing Lin
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Proper citation: Shin Lin, Yiing Lin 2020. Protocol for Freezing in OCT. protocols.io https://dx.doi.org/10.17504/protocols.io.bpx7mprn Copy
Authors: Elizabeth Neumann, Heath Patterson, Jamie Allen, Maya Brewer, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins
Group: VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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.
Proper citation: 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 Copy
Authors: Jeff Spraggins, Elizabeth Neumann, Mark deCaestecker, Danielle Gutierrez, Jamie Allen, Maya Brewer
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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.
Proper citation: 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 Copy
Authors: Marda Jorgensen, Maigan Brusko
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Proper citation: Marda Jorgensen, Maigan Brusko 2020. HuBMAP UF TMC - 10x Genomics scRNAseq Modality Overview . protocols.io https://dx.doi.org/10.17504/protocols.io.be79jhr6 Copy
Authors: Nina Dar, Long Cai
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: Once a tissue is received, it should be frozen using the following protocol:
Proper citation: Nina Dar, Long Cai 2019. Tissue Freezing for seqFISH. protocols.io https://dx.doi.org/10.17504/protocols.io.7mdhk26 Copy
Authors: Kelley Knizner, Christopher Simmons
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research
Summary: 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
Proper citation: 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 Copy
Authors: Maya Brewer, Yuantee Zhu, Danielle Gutierrez, Jeff Spraggins, Mark De Caestecker
Group: VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This protocol describes the process for antibody purification and subsequent labeling for direct immunofluorescence.
Proper citation: 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 Copy
Authors: Michelle Daniel, Marda Jorgensen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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”).
Proper citation: Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Data Acquisition. protocols.io https://dx.doi.org/10.17504/protocols.io.bf2ijqce Copy
Authors: Leigh Propper, Marda Jorgensen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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.
Proper citation: Leigh Propper, Marda Jorgensen 2019. CODEX Microtomy Tracking Sheet. protocols.io https://dx.doi.org/10.17504/protocols.io.baefibbn Copy
Authors: Marda Jorgensen, Michelle Daniel
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: FFPE block are cut into thin sections.
Proper citation: Marda Jorgensen, Michelle Daniel 2020. Cutting FFPE Sections for Imaging Mass Cytometry. protocols.io https://dx.doi.org/10.17504/protocols.io.bfz4jp8w Copy
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