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Authors: Elizabeth Neumann, Jamie Allen, David Anderson, Danielle Gutierrez, Jeff Spraggins
Group: VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: Scope:Acquire 10 μm spatial resolution imaging mass spectrometry (IMS) datasets of ~ 5mm2 regions of tissue.Expected Outcome:A series of ion images that can be used to visualize the distribution of lipids localizing to physiological regions within the human kidney.
Proper citation: Elizabeth Neumann, Jamie Allen, David Anderson, Danielle Gutierrez, Jeff Spraggins 2019. High Resolution Imaging Mass Spectrometry Analysis using Bruker Daltonics Platforms. protocols.io https://dx.doi.org/10.17504/protocols.io.7gdhjs6 Copy
Authors: Marda Jorgensen, Jerelyn Nick, Franchesca Farris, Jesus Penaloza
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This protocol is an overview of all of the protocols currently in use for the CODEX 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.
Proper citation: Marda Jorgensen, Jerelyn Nick, Franchesca Farris, Jesus Penaloza 2020. HuBMAP TMC-Florida/Zurich CODEX Modality Overview. protocols.io https://dx.doi.org/10.17504/protocols.io.be9pjh5n Copy
Authors: Jamie Allen, Jennifer Harvey, Maya Brewer, Mark De Caestecker, Jeff Spraggins
Group: VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: Scope:The PAS stain is used to demonstrate polysaccharides such as glycogen, and mucosubstances such as glycoproteins, glycolipids and mucins in tissues. It is used as a replacement for the H&E in kidney pathology.Expected Outcome:Intermyofibrillar Network…………………………..Pink to RoseGlycogen………………………………………………….…..Pink to RoseMyofibrils……………………………………………………..UnstainedType I fibers………………………………………………….LighterType II fibers…………………………………………………DarkerBlood Vessel walls & connective tissue…..Faintly Stained
Proper citation: Jamie Allen, Jennifer Harvey, Maya Brewer, Mark De Caestecker, Jeff Spraggins 2019. PAS Staining of Fresh Frozen or Paraffin Embedded Human Kidney Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.4qngvve Copy
Authors: Nina Dar, Long Cai, Shin Lin
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Proper citation: Nina Dar, Long Cai, Shin Lin 2019. Coverslips preparation for seqFISH . protocols.io https://dx.doi.org/10.17504/protocols.io.7mihk4e Copy
Authors: Maya Brewer, Jamie Allen, Elizabeth Neumann, Agnes Fogo, Raymond Harris, Danielle Gutierrez, Mark De Caestecker, Jeff Spraggins
Group: VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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.
Proper citation: 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 https://dx.doi.org/10.17504/protocols.io.7gehjte Copy
Authors: Marda Jorgensen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This is the appendix for lymph nodes.
Proper citation: Marda Jorgensen 2020. SOP Appendix for Lymph Node. protocols.io https://dx.doi.org/10.17504/protocols.io.bcwpixdn 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.bc3kiykw Copy
Authors: Franchesca Farris, Marda Jorgensen, Jerelyn Nick, Jesus Peñaloza
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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.
Proper citation: Franchesca Farris, Marda Jorgensen, Jerelyn Nick, Jesus Peñaloza 2020. CODEX Acquisition Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bdifi4bn Copy
Authors: Jerelyn Nick, Franchesca Farris, Marda Jorgensen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: Standard IHC staining, such as this DAB protocol, is included in the validation of new antibodies at the University of Florida Tissue Mapping Center, TMC-Florida/Zurich. This procedure includes all of the reagents necessary to perform a DAB based immunohistochemistry reaction. DAB Substrate (3,3’-diaminobenzidine) produces a brown reaction product in the presence of peroxidase (HRP) enzyme.
Proper citation: Jerelyn Nick, Franchesca Farris, Marda Jorgensen 2020. DAB Staining of FFPE Slides. protocols.io https://dx.doi.org/10.17504/protocols.io.bdiei4be Copy
Authors: John Hickey
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: See our detailed protocol published with the following title: CODEX multiplexed tissue imaging with DNA-conjugated antibodies.
Proper citation: John Hickey 2021. Imaging - Stanford TMC. protocols.io https://dx.doi.org/10.17504/protocols.io.be8qjhvw Copy
Authors: Franchesca Farris, Maigan Brusko
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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.
Proper citation: Franchesca Farris, Maigan Brusko 2020. HuBMAP UF TMC - Single Cell RNA Seq (10x Genomics) Library Preparation and Sequencing . protocols.io https://dx.doi.org/10.17504/protocols.io.bffvjjn6 Copy
Authors: Marda Jorgensen, Jerelyn Nick, Franchesca Farris, Jesus Penaloza
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This protocol is an overview of all of the protocols currently in use for the CODEX 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.
Proper citation: Marda Jorgensen, Jerelyn Nick, Franchesca Farris, Jesus Penaloza 2020. HuBMAP TMC-Florida/Zurich CODEX Modality Overview. protocols.io https://dx.doi.org/10.17504/protocols.io.bdcbi2sn Copy
Authors: Maya Brewer, Yuantee Zhu, Elizabeth Neumann, Danielle Gutierrez, Jeff Spraggins, Mark De Caestecker
Group: VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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.
Proper citation: Maya Brewer, Yuantee Zhu, Elizabeth Neumann, Danielle Gutierrez, Jeff Spraggins, Mark De Caestecker 2019. Multiplex Immunofluorescence on Fresh Frozen Tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.665hhg6 Copy
Authors: Franchesca Farris
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This is an appendix for spleen SOP.
Proper citation: Franchesca Farris 2020. Appendix for Spleen SOP. protocols.io https://dx.doi.org/10.17504/protocols.io.bbcwiixe Copy
Authors: Leigh Propper, Marda Jorgensen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This method details our microtomy (sectioning) process for reasearch specimens involved with HuBMAP.This process follows the microtomy process that follows after receiving, processing, and embedding of research specimens into formalin fixed, paraffin embedded tissue blocks.
Proper citation: Leigh Propper, Marda Jorgensen 2019. HuBMAP Tissue Sectioning for FFPE Specimens. protocols.io https://dx.doi.org/10.17504/protocols.io.bahdib26 Copy
Authors: Marda Jorgensen, Jerelyn Nick
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the paraffin embedding of HuBMAP specimens.
Proper citation: Marda Jorgensen, Jerelyn Nick 2020. HuBMAP: Paraffin Embedding Tissue Samples . protocols.io https://dx.doi.org/10.17504/protocols.io.bam9ic96 Copy
Authors: Seth Currlin
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: 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 thymus tissue approximately 5 mm3 in size.A useful link: http://wiki.claritytechniques.org/index.php/Immunostaining
Proper citation: Seth Currlin 2020. 3D Immunostaining for CLARITY-processed samples. protocols.io https://dx.doi.org/10.17504/protocols.io.bnzdmf26 Copy
Authors: Yiing Lin, Shin Lin
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Proper citation: Yiing Lin, Shin Lin 2020. HuBMAP Donor and Tissue Eligibility Criteria Form v 1.0. protocols.io https://dx.doi.org/10.17504/protocols.io.bqmamu2e Copy
Authors: Marda Jorgensen, Jerelyn Nick
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: The purpose of this Standard Operating Procedure (SOP) is to outline the procedures for processing and storing thymus tissue received for HuBMAP consortium assay and analysis.
Proper citation: Marda Jorgensen, Jerelyn Nick 2020. Case Processing SOP for Thymus . protocols.io https://dx.doi.org/10.17504/protocols.io.bbgmiju6 Copy
Authors: Michelle Daniel, Marda Jorgensen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Proper citation: Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Modality Overview . protocols.io https://dx.doi.org/10.17504/protocols.io.bgatjsen Copy
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