CODEX User Manual
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User Manual – Rev C CODEX® User Manual Rev C 1 Akoya Biosciences, Inc. CODEX® User Manual Revision C, December 2020 © 2020 by Akoya Biosciences, Inc. CODEX® is a trademark of Akoya Biosciences, Inc. All other trademarks are the property of their respective holders. ALL RIGHTS RESERVED. DUPLICATION AND/OR REPRODUCTION OF ALL OR ANY PORTION OF THIS DOCUMENTATION WITHOUT THE EXPRESS WRITTEN CONSENT OF AKOYA BIOSCIENCES, INC. IS STRICTLY FORBIDDEN. DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, AKOYA BIOSCIENCES, INC. AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT. FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES. THE CONTENTS OF THIS DOCUMENT ARE COVERED UNDER NDA. This Protocol is based on current knowledge of the process and is subject to change. Diagrams and pictures are for illustration only and might differ from actual implementation. CODEX® User Manual Rev C 2 Table of Contents CHAPTER 1. CODEX® SOLUTION ______________________________________________________ 7 1.1 CODEX® REAGENTS AND CONSUMABLES .................................................................................................................. 8 1.1.1 Materials Supplied _____________________________________________________________________ 8 1.1.2 Materials Not Supplied _________________________________________________________________ 10 1.2 CODEX® INSTRUMENT ........................................................................................................................................ 14 1.2.1 Performance Specifications _____________________________________________________________ 15 1.2.2 Instrument Requirements ______________________________________________________________ 15 1.3 CODEX® SOFTWARE SUITE .................................................................................................................................. 15 1.3.1 CODEX® Instrument Manager (CIM) ______________________________________________________ 15 1.3.2 CODEX® Processor ____________________________________________________________________ 15 1.3.3 CODEX® Multiplex Analysis Viewer (MAV) _________________________________________________ 15 1.4 SAFETY .............................................................................................................................................................. 15 1.4.1 DMSO ______________________________________________________________________________ 16 1.4.2 Acetone, Ethanol, Methanol, and Paraformaldehyde ________________________________________ 16 1.4.3 Instrumentation ______________________________________________________________________ 16 CHAPTER 2. CODEX® OVERVIEW ____________________________________________________ 17 2.1 CODEX® NOMENCLATURE ................................................................................................................................... 18 2.2 CODEX® TECHNOLOGY........................................................................................................................................ 19 2.3 CODEX® EXPERIMENTAL DESIGN .......................................................................................................................... 19 2.4 PROCEDURAL OVERVIEW ...................................................................................................................................... 21 2.5 USER GUIDE OVERVIEW ....................................................................................................................................... 24 CHAPTER 3. COVERSLIP PREPARATION AND TISSUE SECTIONING _______________________ 25 3.1 POLY-L-LYSINE COVERSLIP PREPARATION ................................................................................................................. 25 3.1.1 Incubating Coverslips __________________________________________________________________ 25 3.1.2 Washing and Storing Coverslips __________________________________________________________ 27 3.2 FRESH-FROZEN TISSUE SECTIONING ........................................................................................................................ 28 3.3 FFPE TISSUE SECTIONING ..................................................................................................................................... 29 CHAPTER 4. ANTIBODY CONJUGATION _______________________________________________ 31 4.1 CONJUGATING ANTIBODIES ................................................................................................................................... 32 4.1.1 Assign a CODEX® Barcode to each antibody that will be conjugated _____________________________ 36 4.1.2 Block non-specific binding of antibody to MWCO filter _______________________________________ 36 4.1.3 Measure and calculate protein concentration ______________________________________________ 36 4.1.4 Concentrate purified antibody solution____________________________________________________ 36 4.1.5 Initiate antibody reduction _____________________________________________________________ 36 4.1.6 Buffer Exchange of the Antibody Solution __________________________________________________ 37 4.1.7 Prepare CODEX® Barcode Solution _______________________________________________________ 37 4.1.8 Set Up Antibody Conjugation Reaction ____________________________________________________ 37 4.1.9 Purify CODEX® Antibody Conjugates ______________________________________________________ 37 CODEX® User Manual Rev C 3 4.1.10 Collect CODEX® Antibody Solution ______________________________________________________ 38 4.2 VALIDATING CUSTOM-CONJUGATED ANTIBODIES (VIA GEL ELECTROPHORESIS) ............................................................... 38 4.2.1 Sample Preparation ___________________________________________________________________ 39 4.2.2 Gel Setup ____________________________________________________________________________ 39 4.2.3 Gel Visualization ______________________________________________________________________ 39 CHAPTER 5. TISSUE STAINING _______________________________________________________ 41 5.1 FRESH-FROZEN TISSUE PRE-STAINING ..................................................................................................................... 42 5.1.1 Plate configuration ____________________________________________________________________ 45 5.1.2 Tissue Retrieval _______________________________________________________________________ 46 5.1.3 Acetone Incubation ___________________________________________________________________ 46 5.1.4 Tissue Drying _________________________________________________________________________ 46 5.1.5 Tissue Hydration ______________________________________________________________________ 47 5.1.6 Fix Tissue ____________________________________________________________________________ 47 5.1.7 Wash the tissue ______________________________________________________________________ 47 5.1.8 Equilibrate Tissue in Staining Buffer ______________________________________________________ 47 5.2 FRESH-FROZEN TISSUE STAINING ............................................................................................................................ 48 5.2.1 Understanding Antibody Dilution ________________________________________________________ 48 5.2.2 Preparation of the Antibody Cocktail Solution ______________________________________________ 48 5.2.3 Tissue Staining _______________________________________________________________________ 49 5.3 FRESH-FROZEN TISSUE POST-STAINING ................................................................................................................... 49 5.3.1 Wash Tissue _________________________________________________________________________ 52 5.3.2 Fix Tissue ____________________________________________________________________________ 53 5.3.3 Wash Tissue _________________________________________________________________________ 53 5.3.4 Ice-cold Methanol Incubation ___________________________________________________________ 53 5.3.5 Wash Tissue _________________________________________________________________________ 54 5.3.6 Fix Tissue ____________________________________________________________________________ 54 5.3.7 Wash Tissue _________________________________________________________________________ 55 5.3.8 Store Tissue __________________________________________________________________________ 55 5.4 FFPE TISSUE PRE-STAINING .................................................................................................................................. 55 5.4.1 Tissue Pre-treatment __________________________________________________________________ 60 5.4.2 Tissue Deparaffinization and Hydration ___________________________________________________ 60 5.4.3 Antigen Retrieval _____________________________________________________________________ 61 5.4.4 Wash Tissue _________________________________________________________________________ 62 5.4.5 Equilibrate Tissue in Staining Buffer ______________________________________________________ 62 5.5 FFPE TISSUE STAINING ........................................................................................................................................ 62 5.5.1 Understanding Antibody Dilution ________________________________________________________ 62 5.5.2 Preparation of the Antibody Cocktail Solution ______________________________________________ 63 5.5.3 Tissue Staining _______________________________________________________________________