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| Name | Authors | DOI | Group |
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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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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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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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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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Imaging Mass Cytometer Tuning Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | 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 dx.doi.org/10.17504/protocols.io.bf2gjqbw | 2021-03-29 03:11:11 | |||
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Light Sheet Fluorescence Microscopy Image Acquisition Resource Report Resource Website |
Seth Currlin, Marda Jorgensen, Jerelyn Nick | 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 dx.doi.org/10.17504/protocols.io.bprsmm6e | 2021-03-29 03:11:31 | |||
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UF H&E Staining Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen | 10.17504/protocols.io.8jthunn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | UF H&E Staining | University of Florida, University of Florida | 1 | 2019 | Franchesca Farris, Marda Jorgensen 2019. UF H&E Staining. protocols.io dx.doi.org/10.17504/protocols.io.8jthunn | 2021-03-29 03:13:22 | |||
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FFPE Tissue Sectioning for CODEX Resource Report Resource Website |
Marda Jorgensen, Franchesca Farris | 10.17504/protocols.io.8mfhu3n | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | FFPE tissues for CODEX® analysis must adhere directly onto Poly-lysine-coated coverslips. Preparation and storage of tissue slices are critical for sample integrity. | University of Florida, University of Florida | 1 | 2019 | Marda Jorgensen, Franchesca Farris 2019. FFPE Tissue Sectioning for CODEX. protocols.io dx.doi.org/10.17504/protocols.io.8mfhu3n | 2021-03-29 03:13:34 | |||
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SOP Appendix for Thymus Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen | 10.17504/protocols.io.bcwgixbw | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This is the appendix for the Thymus SOP. | University of Florida, University of Florida | 2 | 2020 | Franchesca Farris, Marda Jorgensen 2020. SOP Appendix for Thymus . protocols.io dx.doi.org/10.17504/protocols.io.bcwgixbw | 2021-03-29 03:13:42 | |||
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CODEX - Poly-l-Lysine Cover-Slip Preparation Resource Report Resource Website |
Leigh Propper, Franchesca Farris, Marda Jorgensen | 10.17504/protocols.io.baeribd6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Poly-Lysine Coverslip Preparation This section describes the process of creating Poly-lysine-coated coverslips that are used for the tissue sections in the CODEX® experiment workflow. | University of Florida, University of Florida, University of Florida | 2 | 2019 | Leigh Propper, Franchesca Farris, Marda Jorgensen 2019. CODEX - Poly-l-Lysine Cover-Slip Preparation. protocols.io dx.doi.org/10.17504/protocols.io.baeribd6 | 2021-03-29 03:12:40 | |||
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CODEX - Poly-l-Lysine Cover-Slip Preparation Resource Report Resource Website |
Leigh Propper, Franchesca Farris, Marda Jorgensen | 10.17504/protocols.io.baxyifpw | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Poly-Lysine Coverslip Preparation This protocol describes the process of creating Poly-lysine-coated coverslips that are required for mounting tissue sections for the CODEX® experiment workflow. | University of Florida, University of Florida, University of Florida | 3 | 2020 | Leigh Propper, Franchesca Farris, Marda Jorgensen 2020. CODEX - Poly-l-Lysine Cover-Slip Preparation. protocols.io dx.doi.org/10.17504/protocols.io.baxyifpw | 2021-03-29 03:14:55 | |||
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Imaging Mass Cytometry Modality Overview Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | 10.17504/protocols.io.bf3kjqkw | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Unversity of Zurich, University of Florida | 1 | 2020 | Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Modality Overview . protocols.io dx.doi.org/10.17504/protocols.io.bf3kjqkw | 2021-03-29 03:14:08 | ||||
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HuBMAP: Embedding Fixed Frozen OCT Samples Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick | 10.17504/protocols.io.basniede | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the OCT embedding of HuBMAP frozen fixed specimens. | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Jerelyn Nick 2020. HuBMAP: Embedding Fixed Frozen OCT Samples. protocols.io dx.doi.org/10.17504/protocols.io.basniede | 2021-03-29 03:15:13 | |||
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Poly-Lysine Coverslip Preparation Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen | 10.17504/protocols.io.8kthuwn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | 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. | University of Florida, University of Florida | 1 | 2019 | Franchesca Farris, Marda Jorgensen 2019. Poly-Lysine Coverslip Preparation. protocols.io dx.doi.org/10.17504/protocols.io.8kthuwn | 2021-03-29 03:15:21 | |||
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Case Processing SOP for Lymph Nodes Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick | 10.17504/protocols.io.bbgnijve | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The purpose of this Standard Operating Procedure is to outline procedures for processing and storing lymph node tissue received for HuBMAP consortium assay and analysis. | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Jerelyn Nick 2020. Case Processing SOP for Lymph Nodes . protocols.io dx.doi.org/10.17504/protocols.io.bbgnijve | 2021-03-29 03:12:06 | |||
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CODEX Microtomy Tracking Sheet Resource Report Resource Website |
Leigh Propper, Marda Jorgensen | 10.17504/protocols.io.baefibbn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | 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. | University of Florida, University of Florida | 1 | 2019 | Leigh Propper, Marda Jorgensen 2019. CODEX Microtomy Tracking Sheet. protocols.io dx.doi.org/10.17504/protocols.io.baefibbn | 2021-03-29 03:10:16 | |||
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Cutting FFPE Sections for Imaging Mass Cytometry Resource Report Resource Website |
Marda Jorgensen, Michelle Daniel | 10.17504/protocols.io.bfz4jp8w | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | FFPE block are cut into thin sections. | University of Florida, University of Zürich | 1 | 2020 | Marda Jorgensen, Michelle Daniel 2020. Cutting FFPE Sections for Imaging Mass Cytometry. protocols.io dx.doi.org/10.17504/protocols.io.bfz4jp8w | 2021-03-29 03:10:24 |
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