Apr 21, 2020
Version 2
HuBMAP TMC-Florida/Zurich CODEX Modality Overview V.2
- Marda Jorgensen1,
- Jerelyn Nick1,
- Franchesca Farris1,
- Jesus Penaloza1
- 1University of Florida
- Human BioMolecular Atlas Program (HuBMAP) Method Development CommunityTech. support email: Jeff.spraggins@vanderbilt.edu
Protocol Citation: Marda Jorgensen, Jerelyn Nick, Franchesca Farris, Jesus Penaloza 2020. HuBMAP TMC-Florida/Zurich CODEX Modality Overview. protocols.io https://dx.doi.org/10.17504/protocols.io.be9pjh5n
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 17, 2020
Last Modified: October 02, 2020
Protocol Integer ID: 35855
Keywords: HubMAP, TMC-UF/Zurich, CODEX, Multiplex fluorescent Imaging , Lymph node , Thymus , Spleen, CODEX processing, HubMAP Hive Globus,
Abstract
This protocol is an overview of all of the protocols currently in use for the CODEX 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.
Guidelines
This workflow protocol may be interupted at any point.
Steps are permitted to be performed in non-consecutive order.
Repeated runs on the same sample do not require employing the entire protocol sequence.
Materials
Required materials are provided within each linked protocol.
Safety warnings
Follow all safety guidelines provided with individual links within this protocol.
Before start
Confirm sample ID information at the start of each step.
Process donor organs into samples for analysis.
Lymph Node: dx.doi.org/10.17504/protocols.io.bbgnijve
Register organ donor, organs received and common coordinate region information in the HuBMAP UUID generator at https://uuid.hubmapconsortium.org.
Prepare paraffin blocks from tissue samples.
Cassette Processing: dx.doi.org/10.17504/protocols.io.8nzhvf6
Paraffin Embedding: dx.doi.org/10.17504/protocols.io.bam9ic96
Prepare H&E sections for histopathological assessment.
Sectioning: dx.doi.org/10.17504/protocols.io.bahdib26
H&E Staining: dx.doi.org/10.17504/protocols.io.beamjac6
Validate antibodies in all target tissue types by IHC using DAB Staining:
Stain coverslips with Akoya invertoried antibodies.
Make CODEX bar coded reporter trays.
Preparation: dx.doi.org/10.17504/protocols.io.bc2riyd6
Perform multiplex data acquisition using CODEX robot and Keyence microscope.
Acquisition: dx.doi.org/10.17504/protocols.io.bdifi4bn
Transfer images to analysis computer and perform CODEX processing.
Codex_Processor.docx Register completed CODEX section information in the HuBMAP UUID generator at https://uuid.hubmapconsortium.org.
Prepare and upload data to the HuBMAP HIVE Globus using hipergator.
Datasets to HiperGator-Globus.docx