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| Name | Authors | DOI | Group |
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Associated Publications |
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VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN) Resource Report Resource Website |
Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins | DOI:10.17504/protocols.io.bb2wiqfe | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | We aim to develop high resolution, chemically informative imaginig methodologies for building an atlas of human organs, such as the kidney.Scope:Provide an overview of the methods used by the Vanderbilt Tissue Mapping Center as part of the Human Biomolecular Atlas Program (HuBMAP, NIH Common Fund) and contextualize individual protocols within our larger workflow. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center, Vanderbilt University, Vanderbilt University | 2 | 2020 | Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins 2020. VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN). protocols.io https://dx.doi.org/10.17504/protocols.io.bb2wiqfe | 2021-04-15 09:14:25 | |||
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CODEX - Poly-l-Lysine Cover-Slip Preparation Resource Report Resource Website |
Leigh Propper, Franchesca Farris, Marda Jorgensen | DOI: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 https://dx.doi.org/10.17504/protocols.io.baeribd6 | 2021-04-15 09:14:27 | |||
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HuBMAP Tissue Preservation Protocol v2 Resource Report Resource Website |
Yiing Lin, Shin Lin | DOI:10.17504/protocols.io.bqm5mu86 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Washington University, St. Louis, University of Washington | 1 | 2020 | Yiing Lin, Shin Lin 2020. HuBMAP Tissue Preservation Protocol v2. protocols.io https://dx.doi.org/10.17504/protocols.io.bqm5mu86 | 2021-04-15 09:14:36 | ||||
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Storage and Processing of Tissue for bulk RNA Isolation Resource Report Resource Website |
Aaron Horning | DOI:10.17504/protocols.io.bf52jq8e | NCIHTAN, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Stanford University | 1 | 2020 | Aaron Horning 2020. Storage and Processing of Tissue for bulk RNA Isolation. protocols.io https://dx.doi.org/10.17504/protocols.io.bf52jq8e | 2021-04-15 09:14:31 | ||||
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LC-MS/MS Label-Free Proteomic Data Acquisition Resource Report Resource Website |
Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins | DOI:10.17504/protocols.io.bs7hnhj6 | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Description of settings used to acquire LC-MS/MS data from label-free proteomic samples. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 4 | 2021 | Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins 2021. LC-MS/MS Label-Free Proteomic Data Acquisition. protocols.io https://dx.doi.org/10.17504/protocols.io.bs7hnhj6 | 2021-04-15 09:14:36 | |||
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Preparation of Adult Human Kidney Tissue for Single Nucleus RNA-seq and Other Multiomics Studies Resource Report Resource Website |
Sanjay Jain, Masato Hoshi, Amanda Knoten, Diane Salamon | DOI:10.17504/protocols.io.568g9hw | KPMP, Human BioMolecular Atlas Program (HuBMAP) Method Development Community, Jain Lab | Critical to generating robust single cell or tissue gene expression data is ensuring that the source samples are procured and processed in a way that minimizes artifacts. This is especially critical for generating single cell/nucleus gene expression data from adult human tissue samples that are difficult to dissociate and might require prolonged manipulations that will introduce stress response signatures. We describe methods to: minimize these unwanted processing effects to enable interrogation of limited tissues, such as biopsies; allow histological validation and quality assurance and control of the samples; ensure compatibility with both single cell assays and orthogonal technologies. This involves preparing fresh frozen O.C.T. embedded tissue cryoblocks to collect thick sections for gene expression studies and adjacent sections for QA/QC, bulk RNAseq, DNA preparation or multiplex in situ RNA hybridization. The protocol for embedding limited amount of tissue for cryosections and susequent OMICS studies should be applicable to several solid organs and biopsies. | Washington University School of Medicine, Saint Louis, MO, Washington University, Washington University, Washington University | https://rdcu.be/bPe70 | 1 | 2019 | Sanjay Jain, Masato Hoshi, Amanda Knoten, Diane Salamon 2019. Preparation of Adult Human Kidney Tissue for Single Nucleus RNA-seq and Other Multiomics Studies. protocols.io https://dx.doi.org/10.17504/protocols.io.568g9hw | 2021-04-15 09:14:36 | ||
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VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN) Resource Report Resource Website |
Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins | DOI:10.17504/protocols.io.beevjbe6 | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | We aim to develop high resolution, chemically informative imaginig methodologies for building an atlas of human organs, such as the kidney.Scope:Provide an overview of the methods used by the Vanderbilt Tissue Mapping Center as part of the Human Biomolecular Atlas Program (HuBMAP, NIH Common Fund) and contextualize individual protocols within our larger workflow. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center, Vanderbilt University, Vanderbilt University | 3 | 2020 | Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins 2020. VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN). protocols.io https://dx.doi.org/10.17504/protocols.io.beevjbe6 | 2021-04-15 09:14:38 | |||
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seqFISH Tissue Preservation Resource Report Resource Website |
Long Cai, Nina Dar, Yiing Lin, Shin Lin | DOI:10.17504/protocols.io.7e7hjhn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Tissue Preparation for seqFISH | California Institute of Technology, California Institute of Technology, Washington University, Saint Louis, University of Washington | 3 | 2019 | Long Cai, Nina Dar, Yiing Lin, Shin Lin 2019. seqFISH Tissue Preservation. protocols.io https://dx.doi.org/10.17504/protocols.io.7e7hjhn | 2021-04-15 09:14:43 | |||
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UF H&E Staining Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen | DOI: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 https://dx.doi.org/10.17504/protocols.io.8jthunn | 2021-04-15 09:15:00 | |||
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Cryostat Sectioning of Tissues for 3D Multimodal Molecular Imaging Resource Report Resource Website |
David Anderson, Elizabeth Neumann, Jamie Allen, Maya Brewer, Danielle Gutierrez, Jeff Spraggins | DOI:10.17504/protocols.io.7ethjen | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope: Protocol for sectioning flash frozen tissue that can be used for 3D IMS or MxIF experiments.Expected Outcome:Serial sections from a tissue that IMS and MxIF can be performed on with subsequent 3D reconstruction | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 1 | 2019 | David Anderson, Elizabeth Neumann, Jamie Allen, Maya Brewer, Danielle Gutierrez, Jeff Spraggins 2019. Cryostat Sectioning of Tissues for 3D Multimodal Molecular Imaging. protocols.io https://dx.doi.org/10.17504/protocols.io.7ethjen | 2021-04-15 09:14:44 | |||
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SOP Appendix for Thymus Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen | DOI: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 https://dx.doi.org/10.17504/protocols.io.bcwgixbw | 2021-04-15 09:14:48 | |||
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Human Kidney, Urinary Tract, and Lung Cell Type Mapping Pipeline for the Human Biomolecular Atlas Program (HuBMAP) Resource Report Resource Website |
Blue Lake, Elizabeth Duong, Dinh Diep, Xin Sun, Peter K, Jim Hagood, Gloria Pryhuber, Sanjay Jain, Kun Zhang [University Of California | DOI:10.17504/protocols.io.bj9wkr7e | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This document provides an overview of the protocols used by the Human Kidney, Urinary Tract, and Lung Mapping Center (KULMAP) for generation of spatially resolved mulitomic cell type organ maps within HuBMAP. This involves sequencing of the transcriptomes and epigenomes of dissociated single cells in a massively parallel manner, which will then inform on a highly multiplexed RNA in situ imaging method (DART-FISH) for spatial mapping of hundreds of molecular targets in the tissue sections, at a subcellular resolution. These spatial molecular maps will serve as scaffolds for computational registration of cell types and the associated transcriptome/chromatin maps to the tissue space. | University of California, San Diego, University of California, San Diego, University of California, San Diego, University of California, San Diego, Harvard Medical School, University of North Carolina at Chapel Hill, University of Rochester Medical Center, Washington University, Saint Louis, University of California, San Diego | 1 | 2020 | Blue Lake, Elizabeth Duong, Dinh Diep, Xin Sun, Peter K, Jim Hagood, Gloria Pryhuber, Sanjay Jain, Kun Zhang [University Of California 2020. Human Kidney, Urinary Tract, and Lung Cell Type Mapping Pipeline for the Human Biomolecular Atlas Program (HuBMAP). protocols.io https://dx.doi.org/10.17504/protocols.io.bj9wkr7e | 2021-04-15 09:15:15 | |||
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Lightsheet Microscope Acquisition Protocol Resource Report Resource Website |
Marda Jorgensen, Seth Currlin | DOI:10.17504/protocols.io.begajbse | 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 lightsheet 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 lightsheet 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 lightsheet 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 lasersheet 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 lightsheet alignment | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Seth Currlin 2020. Lightsheet Microscope Acquisition Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.begajbse | 2021-04-15 09:15:12 | |||
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HuBMAP TMC-Florida/Zurich Light Sheet Fluorescence Microscopy Modality Overview Resource Report Resource Website |
Jerelyn Nick, Marda Jorgensen, Seth Currlin | DOI:10.17504/protocols.io.bqaamsae | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This protocol is an overview of all of the protocols currently in use for the Light Sheet Fluorescence Microscopy 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. | University of Florida, University of Florida, University of Florida | 1 | 2020 | Jerelyn Nick, Marda Jorgensen, Seth Currlin 2020. HuBMAP TMC-Florida/Zurich Light Sheet Fluorescence Microscopy Modality Overview. protocols.io https://dx.doi.org/10.17504/protocols.io.bqaamsae | 2021-04-15 09:14:49 | |||
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VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN) Resource Report Resource Website |
Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins | DOI:10.17504/protocols.io.bfskjncw | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | We aim to develop high resolution, chemically informative imaginig methodologies for building an atlas of human organs, such as the kidney.Scope:Provide an overview of the methods used by the Vanderbilt Tissue Mapping Center as part of the Human Biomolecular Atlas Program (HuBMAP, NIH Common Fund) and contextualize individual protocols within our larger workflow. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center, Vanderbilt University, Vanderbilt University | 4 | 2020 | Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins 2020. VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN). protocols.io https://dx.doi.org/10.17504/protocols.io.bfskjncw | 2021-04-15 09:14:52 | |||
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Image Registration of MALDI IMS to Microscopy Resource Report Resource Website |
Nathan Heath Patterson, Elizabeth Neumann, Jamie Allen, Danielle Gutierrez, Jeff Spraggins | DOI:10.17504/protocols.io.bed2ja8e | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:To process to register MALDI IMS images to different types of microscopy images. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 1 | 2020 | Nathan Heath Patterson, Elizabeth Neumann, Jamie Allen, Danielle Gutierrez, Jeff Spraggins 2020. Image Registration of MALDI IMS to Microscopy. protocols.io https://dx.doi.org/10.17504/protocols.io.bed2ja8e | 2021-04-15 09:15:12 | |||
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Library Generation using Slide-seqV2 Resource Report Resource Website |
Robert Stickels, Evan Murray, Jamie Marshall, Karol Balderrama, Irving Barrera, Evan Macosko, Fei Chen | DOI:10.17504/protocols.io.bpgzmjx6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This is a protocol detailing the steps necessary to generate libraries using previously manufactured Slide-seq arrays. | Broad Institute of MIT and Harvard, Harvard Univers, Broad Institute of MIT and Harvard, Broad Institute of MIT and Harvard, Broad Institute of MIT and Harvard, Broad Institute of MIT and Harvard, Broad Institute of MIT and Harvard, Broad Institute of MIT and Harvard | 1 | 2020 | Robert Stickels, Evan Murray, Jamie Marshall, Karol Balderrama, Irving Barrera, Evan Macosko, Fei Chen 2020. Library Generation using Slide-seqV2. protocols.io https://dx.doi.org/10.17504/protocols.io.bpgzmjx6 | 2021-04-15 09:15:14 | |||
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UF / HuBMAP - H&E Staining Process Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen, Leigh Propper | DOI:10.17504/protocols.io.9qbh5sn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This protocol will detail our method of utilizing the H&E stain as a nonspecific entity to achieve optimal results in our staining process for our research samples.Hematoxylin and Eosin stains are used in many areas of the laboratory, including frozen sections, fine needle aspirates, and paraffin fixed embedded tissues. There are multiple factors involved in determining what makes a well stained slide, and one of the primary factors involved in the final product is pathologist preference. Other important factors also play important roles in your final stain, such as reagents and their quality, consistency, initial microtomy quality and selecting a sound procedure. Hematoxylin is used to illustrate nuclear detail in cells. The resulting intensity and shade of the dye in the cells is primarily reliant on the length of time the sample spends in hematoxylin. The cytoplasmic component of the section is brought out by Eosin, which is the most commonly used counterstain in histology. It's varying shades of pink and red provide an exceptional contrast between the nuclear and cytoplasmic areas of interest. | University of Florida, University of Florida, University of Florida | 2 | 2019 | Franchesca Farris, Marda Jorgensen, Leigh Propper 2019. UF / HuBMAP - H&E Staining Process . protocols.io https://dx.doi.org/10.17504/protocols.io.9qbh5sn | 2021-04-15 09:15:39 | |||
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HuBMAP - Tissue Processing with Paraffin Infiltration Resource Report Resource Website |
Marda Jorgensen, Franchesca Farris, Jerelyn Nick | DOI:10.17504/protocols.io.8nzhvf6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the automated processing of formalin fixed HuBMAP specimens for paraffin embedding. | University of Florida, University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Franchesca Farris, Jerelyn Nick 2020. HuBMAP - Tissue Processing with Paraffin Infiltration. protocols.io https://dx.doi.org/10.17504/protocols.io.8nzhvf6 | 2021-04-15 09:15:18 | |||
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CODEX Antibody Staining Protocol for FFPE tissues Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick | DOI: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 https://dx.doi.org/10.17504/protocols.io.bbsdina6 | 2021-04-15 09:15:22 |
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