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Authors: Robert Stickels, Evan Murray, Jamie Marshall, Karol Balderrama, Irving Barrera, Evan Macosko, Fei Chen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This is a protocol detailing the steps necessary to generate libraries using previously manufactured Slide-seq arrays.
Proper citation: Robert Stickels, Evan Murray, Jamie Marshall, Karol Balderrama, Irving Barrera, Evan Macosko, Fei Chen 2020. Library Generation using Slide-seqV2. protocols.io dx.doi.org/10.17504/protocols.io.bpgzmjx6 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 dx.doi.org/10.17504/protocols.io.8kthuwn 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. Sample prep - Stanford TMC. protocols.io dx.doi.org/10.17504/protocols.io.be9zjh76 Copy
Authors: Marda Jorgensen, Jerelyn Nick
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 lymph node tissue received for HuBMAP consortium assay and analysis.
Proper citation: Marda Jorgensen, Jerelyn Nick 2020. Case Processing SOP for Lymph Nodes . protocols.io dx.doi.org/10.17504/protocols.io.bbgnijve Copy
Authors: yang1832 , Julia Laskin
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, NanoDESI MSI Julia Laskin group Purdue
Summary: Our goal is to map the biological tissues with Nano-DESI Mass Spectrometry Imaging and build an atlas of human kidney.Scope: Provide an overview of the sample preparation steps used by the Vanderbilt Tissue Mapping Center and Nano-DESI MSI workflow used by Julia Laskin's group as part of the Human Biomolecular Atlas Program (HuBMAP, NIH Common Fund).
Proper citation: yang1832 , Julia Laskin 2020. Nano-DESI Mass Spectrometry Imaging kidney characterization pipeline for tissues collected by Vanderbilt University. protocols.io dx.doi.org/10.17504/protocols.io.bmwik7ce 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 dx.doi.org/10.17504/protocols.io.baefibbn 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 dx.doi.org/10.17504/protocols.io.bqmamu2e 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 dx.doi.org/10.17504/protocols.io.bfz4jp8w 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 dx.doi.org/10.17504/protocols.io.bbgmiju6 Copy
Authors: Michelle Daniel, Marda Jorgensen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This SOP describes the slide acquisition for spill-over correction of Imaging MassCytometry experiments. The protocol makes use of the compensation slide, which wasprepared previously following the SOP:“HuBMAP_Protocol_3_Compensation_Slide_Preparation.pdf” to measure eachconjugated antibody individually and to record all observed spill-over. The resultingcompensation matrix can be used to compensate data that has been recorded using thesame antibody conjugates.
Proper citation: Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Compensation Slide Acquisition. protocols.io dx.doi.org/10.17504/protocols.io.bf2jjqcn Copy
Authors: Jerelyn Nick, Marda Jorgensen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: A CODEX® Reporter is a fluorescent dye conjugated to an oligonucleotide that is complementary to a specific oligonucleotide barcoded antibody. This protocol describes how to prepare 96-well plates of Reporter Mix for use in a CODEX® run. Each well contains Reporters are grouped together in mixtures of three per cycle plus the nuclear stain. During each cycle the Codex instrument dispenses one well on the tissue sample and images the 3 markers and the nuclear stain. At the end of the cycle the Reporters are removed from the tissue by a gentle wash.
Proper citation: Jerelyn Nick, Marda Jorgensen 2020. CODEX Preparation of Reporter 96-Well Plates. protocols.io dx.doi.org/10.17504/protocols.io.bc2riyd6 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 dx.doi.org/10.17504/protocols.io.bqjimuke 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 dx.doi.org/10.17504/protocols.io.7mihk4e 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 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 dx.doi.org/10.17504/protocols.io.be79jhr6 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 dx.doi.org/10.17504/protocols.io.bam9ic96 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 dx.doi.org/10.17504/protocols.io.bf2ijqce 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 dx.doi.org/10.17504/protocols.io.bnzdmf26 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 dx.doi.org/10.17504/protocols.io.667hhhn 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 dx.doi.org/10.17504/protocols.io.bcwpixdn Copy
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