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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Isolation of single nuclei from solid tissues Resource Report Resource Website |
Blue Lake, Kun Zhang | 10.17504/protocols.io.ufketkw | Human Cell Atlas Method Development Community, KPMP, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | 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. | University of California, San Diego, University of California, San Diego | http://genome-tech.ucsd.edu/ZhangLab/ | 1 | 2019 | Blue Lake, Kun Zhang 2019. Isolation of single nuclei from solid tissues. protocols.io dx.doi.org/10.17504/protocols.io.ufketkw | 2021-03-29 03:07:40 | ||
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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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Initial Rapid Pathology Assessment of Kidney Tissue Resource Report Resource Website |
Jamie Allen, Elizabeth Neumann, Maya Brewer, Haichun Yang, Jeff Spraggins, Danielle Gutierrez | 10.17504/protocols.io.9dph25n | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:Prepare formalin fixed tissue with freezing fresh tissue protocol (dx.doi.org/10.17504/protocols.io.6wghfbw). This protocol provides the steps to prepare formalin fixed human kidney tissue and perform histology assessment for normalcy.Expected Outcome:Pathological assessment of kidney tissue for use in LC-MS/MS and imaging. | Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University, Vanderbilt University | 1 | 2020 | Jamie Allen, Elizabeth Neumann, Maya Brewer, Haichun Yang, Jeff Spraggins, Danielle Gutierrez 2020. Initial Rapid Pathology Assessment of Kidney Tissue. protocols.io dx.doi.org/10.17504/protocols.io.9dph25n | 2021-03-29 03:11:39 | |||
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Automated, Rapid Preparation of Tissue Sections for Proteomic Analysis Resource Report Resource Website |
Jamie Allen, Jeff Spraggins, Danielle Gutierrez | 10.17504/protocols.io.z3pf8mn | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Scope:To describe the procedure for the lysis, reduction/alkylation, trypsin digestion, and clean-up of tissue. Lysis will cover the lysing of tissue and protein concentration. Acetone precipitation will cover the precipitation of proteins. Digestion will cover the process for digesting 100 µg of protein using the Agilent AssayMap Bravo Robot and Promega Rapid Trypsin/LysC. The clean-up of the cells will cover the desalting process on the Agilent AssayMap Bravo and the subsequent preparation of the samples for LC/MS peptide analysis.Expected Outcome/Data:Cell samples lysed, digested, and desalted for analysis on MS instrument. Samples to be analyzed within one or two days of desalting. | Vanderbilt University, Vanderbilt University, Vanderbilt University | https://www.thermofisher.com/order/catalog/product/23225 | 1 | 2019 | Jamie Allen, Jeff Spraggins, Danielle Gutierrez 2019. Automated, Rapid Preparation of Tissue Sections for Proteomic Analysis. protocols.io dx.doi.org/10.17504/protocols.io.z3pf8mn | 2021-03-29 03:11:43 | ||
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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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seqFISH Tissue Preservation Resource Report Resource Website |
Long Cai, Nina Dar, Yiing Lin, Shin Lin | 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 dx.doi.org/10.17504/protocols.io.7e7hjhn | 2021-03-29 03:13:27 | |||
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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 | 10.17504/protocols.io.bbgkijuw | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This is the appendix for the Thymus SOP. | University of Florida | 1 | 2020 | Franchesca Farris 2020. SOP Appendix for Thymus . protocols.io dx.doi.org/10.17504/protocols.io.bbgkijuw | 2021-03-29 03:13:43 | |||
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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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seqFISH Hyb Station Resource Report Resource Website |
Long Cai, Linus Eng, Nico Pierson, Chris Cronin | 10.17504/protocols.io.bhfkj3kw | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The seqFISH Hyb Station is a custom built platform consists of a liquid handling pump , a fluidic switcher , and a 96-well plate auto-sampler which aids seqFISH experiments by flowing hybridization reagents and washes in and out of a flow cell containing the biological sample. Researchers set up multi-day experiments to perform chemistries such as hybridizations, washes, and stripping. In each round of hybridization, the auto sampler handle will move to the designated well and approximately 100uL of readouts reagents are flowed into the custom made flow cell to allow hybridization. Following by imaging with a fluorescent microscope, the signals are extinguished by flowing in excess high formamide solution to melt away the readout probes. These steps are repeated until all hybridization rounds are completed. The controls of seqFISH Hyb Station and imaging are controlled and integrated using the open source software Micro-Manager. | California Institute of Technology, California Institute of Technology, California Institute of Technology, California Institute of Technology | 1 | 2020 | Long Cai, Linus Eng, Nico Pierson, Chris Cronin 2020. seqFISH Hyb Station. protocols.io dx.doi.org/10.17504/protocols.io.bhfkj3kw | 2021-03-29 03:13:42 | |||
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HuBMAP Tissue Preservation Protocol v2 Resource Report Resource Website |
Yiing Lin, Shin Lin | 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 dx.doi.org/10.17504/protocols.io.bqm5mu86 | 2021-03-29 03:12:42 | ||||
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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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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 | 10.17504/protocols.io.7hhhj36 | 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 | 1 | 2019 | Elizabeth Neumann, Jamie Allen, Maya Brewer, David Anderson, Mark De Caestecker, Danielle Gutierrez, Jeff Spraggins 2019. VU Biomolecular Multimodal Imaging Center (BIOMIC) kidney characterization pipeline for tissues collected through the Cooperative Human Tissue Network (CHTN). protocols.io dx.doi.org/10.17504/protocols.io.7hhhj36 | 2021-03-29 03:12:54 | |||
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LC-MS/MS Label-Free Proteomic Data Acquisition Resource Report Resource Website |
Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins | 10.17504/protocols.io.bft3jnqn | 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 | 3 | 2020 | Danielle Gutierrez, Jamie Allen, Zach Jenkins, Jeff Spraggins 2020. LC-MS/MS Label-Free Proteomic Data Acquisition. protocols.io dx.doi.org/10.17504/protocols.io.bft3jnqn | 2021-03-29 03:14:29 | |||
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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 | 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 dx.doi.org/10.17504/protocols.io.bed2ja8e | 2021-03-29 03:14:54 | |||
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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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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 | 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 dx.doi.org/10.17504/protocols.io.568g9hw | 2021-03-29 03:13:04 | ||
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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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