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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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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 | 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 dx.doi.org/10.17504/protocols.io.bpgzmjx6 | 2021-03-29 03:15:12 | |||
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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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Sample prep - Stanford TMC Resource Report Resource Website |
John Hickey | 10.17504/protocols.io.be9zjh76 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | See our detailed protocol published with the following title: CODEX multiplexed tissue imaging with DNA-conjugated antibodies. | Stanford University | 1 | 2021 | John Hickey 2021. Sample prep - Stanford TMC. protocols.io dx.doi.org/10.17504/protocols.io.be9zjh76 | 2021-03-29 03:12:06 | |||
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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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Nano-DESI Mass Spectrometry Imaging kidney characterization pipeline for tissues collected by Vanderbilt University Resource Report Resource Website |
yang1832 , Julia Laskin | 10.17504/protocols.io.bmwik7ce | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, NanoDESI MSI Julia Laskin group Purdue | 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). | Purdue University, Purdue University | 1 | 2020 | 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 | 2021-03-29 03:12:10 | |||
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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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HuBMAP Donor and Tissue Eligibility Criteria Form v 1.0 Resource Report Resource Website |
Yiing Lin, Shin Lin | 10.17504/protocols.io.bqmamu2e | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Washington University, St. Louis, University of Washington | 1 | 2020 | 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 | 2021-03-29 03:10:22 | ||||
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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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Case Processing SOP for Thymus Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick | 10.17504/protocols.io.bbgmiju6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | 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. | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Jerelyn Nick 2020. Case Processing SOP for Thymus . protocols.io dx.doi.org/10.17504/protocols.io.bbgmiju6 | 2021-03-29 03:10:29 | |||
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Imaging Mass Cytometry Compensation Slide Acquisition Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | 10.17504/protocols.io.bf2jjqcn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | 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. | University of Zürich, Unversity of Florida | 1 | 2020 | Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Compensation Slide Acquisition. protocols.io dx.doi.org/10.17504/protocols.io.bf2jjqcn | 2021-03-29 03:11:59 | |||
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CODEX Preparation of Reporter 96-Well Plates Resource Report Resource Website |
Jerelyn Nick, Marda Jorgensen | 10.17504/protocols.io.bc2riyd6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | 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. | University of Florida, University of Florida | 1 | 2020 | Jerelyn Nick, Marda Jorgensen 2020. CODEX Preparation of Reporter 96-Well Plates. protocols.io dx.doi.org/10.17504/protocols.io.bc2riyd6 | 2021-03-29 03:12:01 | |||
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HuBMAP | GE/UPitt Cell DIVE™ Modality Overview Resource Report Resource Website |
Liz McDonough | 10.17504/protocols.io.bqjimuke | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | 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. | GE Research | 1 | 2021 | Liz McDonough 2021. HuBMAP | GE/UPitt Cell DIVE™ Modality Overview. protocols.io dx.doi.org/10.17504/protocols.io.bqjimuke | 2021-03-29 03:08:16 | |||
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Coverslips preparation for seqFISH Resource Report Resource Website |
Nina Dar, Long Cai, Shin Lin | 10.17504/protocols.io.7mihk4e | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | California Institute of Technology, California Institute of Technology, University of Washington | 1 | 2019 | Nina Dar, Long Cai, Shin Lin 2019. Coverslips preparation for seqFISH . protocols.io dx.doi.org/10.17504/protocols.io.7mihk4e | 2021-03-29 03:08:18 | ||||
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Freezing Fresh Tissue Resource Report Resource Website |
Jeff Spraggins, Elizabeth Neumann, Mark deCaestecker, Danielle Gutierrez, Jamie Allen, Maya Brewer | 10.17504/protocols.io.4smgwc6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | 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. | Vanderbilt University, Vanderbilt University, Vanderbilt University Medical Center, Vanderbilt University, Vanderbilt University, Vanderbilt University | 1 | 2019 | 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 | 2021-03-29 03:09:31 | |||
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HuBMAP UF TMC - 10x Genomics scRNAseq Modality Overview Resource Report Resource Website |
Marda Jorgensen, Maigan Brusko | 10.17504/protocols.io.be79jhr6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Maigan Brusko 2020. HuBMAP UF TMC - 10x Genomics scRNAseq Modality Overview . protocols.io dx.doi.org/10.17504/protocols.io.be79jhr6 | 2021-03-29 03:09:30 | ||||
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HuBMAP: Paraffin Embedding Tissue Samples Resource Report Resource Website |
Marda Jorgensen, Jerelyn Nick | 10.17504/protocols.io.bam9ic96 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | The purpose of this Standard Operating Procedure (SOP) is to outline procedures for the paraffin embedding of HuBMAP specimens. | University of Florida, University of Florida | 1 | 2020 | Marda Jorgensen, Jerelyn Nick 2020. HuBMAP: Paraffin Embedding Tissue Samples . protocols.io dx.doi.org/10.17504/protocols.io.bam9ic96 | 2021-03-29 03:09:40 | |||
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Imaging Mass Cytometry Data Acquisition Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | 10.17504/protocols.io.bf2ijqce | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | 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”). | University of Zürich, University of Florida | 1 | 2020 | Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Data Acquisition. protocols.io dx.doi.org/10.17504/protocols.io.bf2ijqce | 2021-03-29 03:09:41 | |||
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3D Immunostaining for CLARITY-processed samples Resource Report Resource Website |
Seth Currlin | 10.17504/protocols.io.bnzdmf26 | 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 thymus tissue approximately 5 mm3 in size.A useful link: http://wiki.claritytechniques.org/index.php/Immunostaining | University of Florida | 1 | 2020 | Seth Currlin 2020. 3D Immunostaining for CLARITY-processed samples. protocols.io dx.doi.org/10.17504/protocols.io.bnzdmf26 | 2021-03-29 03:09:53 | |||
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Antibody Purification and Labeling Resource Report Resource Website |
Maya Brewer, Yuantee Zhu, Danielle Gutierrez, Jeff Spraggins, Mark De Caestecker | 10.17504/protocols.io.667hhhn | VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This protocol describes the process for antibody purification and subsequent labeling for direct immunofluorescence. | Vanderbilt University, Vanderbilt University Medical Center, Vanderbilt University, Vanderbilt University, Division of Nephrology, Vanderbilt University Medical Center | 1 | 2019 | 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 | 2021-03-29 03:09:52 | |||
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SOP Appendix for Lymph Node Resource Report Resource Website |
Marda Jorgensen | 10.17504/protocols.io.bcwpixdn | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This is the appendix for lymph nodes. | University of Florida | 1 | 2020 | Marda Jorgensen 2020. SOP Appendix for Lymph Node. protocols.io dx.doi.org/10.17504/protocols.io.bcwpixdn | 2021-03-29 03:08:34 |
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