Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1
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Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein For use with: Chromium Next GEM Single Cell 3' HT Kit v3.1 48 rxns PN-1000348 | 8 rxns PN-1000370 Chromium Next GEM Chip M Single Cell Kit* 80 rxns PN-1000349 | 16 rxns PN-1000371 (*Included with Chromium Next GEM Single Cell 3' HT Kit v3.1; 16 rxn kit can also be ordered separately) 3' Feature Barcode Kit 16 rxns PN-1000262 Dual Index Kit TT Set A 96 rxns PN-1000215 Dual Index Kit NT Set A 96 rxns PN-1000242

User Guide | Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) Notices Document Number CG000417 | Rev D Legal Notices © 2022 10x Genomics, Inc. (10x Genomics). All rights reserved. Duplication and/or reproduction of all or any portion of this document without the express written consent of 10x Genomics, is strictly forbidden. Nothing contained herein shall constitute any warranty, express or implied, as to the performance of anyproducts described herein. Any and all warranties applicable to any products are set forth in the applicable terms and conditions of sale...

User Guide | Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) Document Revision Summary Document Number CG000417 | Rev D Title Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein Revision Date September 26, 2022 Specific Changes l Updated Thermal Cycler recommendations. General Changes Updated for general minor consistency of language and terms throughout.

User Guide | Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) Table of Contents Introduction Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 10x Genomics Accessories Recommended Thermal Cyclers Additional Kits, Reagents & Equipment Protocol Steps & Timing Stepwise Objectives Cell Surface Protein Labeling Guidelines Tips & Best Practices Step 1: GEM Generation and Barcoding 1.0 Get Started 1.1 Prepare Master Mix Assemble Chromium Next GEM Chip M Sample Loading Guidelines 1.2 Load Chromium Next GEM Chip M 1.3 Run Chromium X GEM Transfer Overview 1.4 Transfer GEMs 1.5...

User Guide | Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) Table of Contents 3.1 Fragmentation, End Repair & A-tailing 3.2 Post Fragmentation, End Repair & A-tailing Double Sided – SPRIselect 3.3 Adaptor Ligation 3.4 Post Ligation Cleanup – SPRIselect 3.5 Sample Index PCR 3.6 Post Sample Index PCR Double Sided Size Selection – SPRIselect 3.7 Post Library Construction QC Step 4: Cell Surface Protein Library Construction 4.0 Get Started 4.1 Sample Index PCR 4.2 Post Sample Index PCR Size Selection – SPRIselect 4.3 Post Library Construction QC Step 5: Sequencing Sequencing...

Introduction Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 Recommended Thermal Cyclers Additional Kits, Reagents & Equipment Protocol Steps & Timing Stepwise Objectives Cell Surface Protein Labeling Guidelines

User Guide | Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 Refer to SDS for handling and disposal information Chromium Next GEM Single Cell 3' HT Kit v3.1, 48 rxns PN-1000348 Chromium Next GEM Single Cell 3’ HT GEM Kit v3.1 48 rxns, PN-1000351 Store at -20°C # PN Library Construction Kit 48 rxns, PN-1000352 Store at -20°C Fragmentation Enzyme Fragmentation Buffer Template Switch Oligo Ligation Buffer Cleanup Buffer Adaptor Oligos cDNA Primers Chromium Next GEM Single Cell 3’ HT Gel Bead Kit v3.1 48 rxns, PN-1000350...

User Guide | Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) Chromium Next GEM Chip M Single Cell Kit, 80 rxns PN-1000349 Chromium Partitioning Oil Store at ambient temperature # PN Partitioning Oil Chromium Recovery Agent Store at ambient temperature # PN Recovery Agent Chromium Next GEM Chip M & Gaskets Store at ambient temperature Chromium Next GEM Chip M Chip Gasket, HT, 5-pack

User Guide | Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) Chromium Next GEM Single Cell 3' HT Kit v3.1, 8 rxns PN-1000370 Chromium Next GEM Single Cell 3’ HT GEM Kit v3.1 8 rxns, PN-1000373 Store at -20°C # PN Library Construction Kit 16 rxns, PN-1000190 Store at -20°C Fragmentation Enzyme Fragmentation Buffer Template Switch Oligo 1 Ligation Buffer Cleanup Buffer Adaptor Oligos cDNA Primers Chromium Next GEM Single Cell 3’ HT Gel Bead Kit v3.1 8 rxns, PN-1000372 Store at -80°C # PN Single Cell 3’ HT Gel Beads v3.1 1 2000443 (8 rxns) Dynabeads TM MyOne TM SILANE...

User Guide | Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) Chromium Next GEM Chip M Single Cell Kit, 16 rxns PN-1000371 Chromium Partitioning Oil Store at ambient temperature # PN Partitioning Oil Chromium Recovery Agent Store at ambient temperature # PN Recovery Agent Chromium Next GEM Chip M & Gaskets Store at ambient temperature Chromium Next GEM Chip M Chip Gasket, HT, 2-pack

User Guide | Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) 3' Feature Barcode Kit, 16 rxns PN-1000262 Two 3' Feature Barcode 16 rxn kits are required for processing 16 samples. 3’ Feature Barcode Kit 16 rxns, PN-1000262 Store at -20°C Feature cDNA Primers 1 Feature cDNA Primers 2 Feature cDNA Primers 3 Dual Index Kit TT Set A, 96 rxns PN-1000215 Dual Index Kit TT Set A Store at -20°C Dual Index Plate TT Set A Dual Index Kit NT Set A, 96 rxns PN-1000242 Dual Index Kit NT Set A Store at -20°C Dual Index Plate NT Set A

User Guide | Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) 10x Genomics Accessories Product Part Number Part Number (Item) Chromium X Chip Holder Recommended Thermal Cyclers The table below lists the thermal cyclers that have been validated by 10x Genomics. Thermal cyclers used must support uniform heating of 100 µl emulsion volumes Part Number C1000 Touch Thermal Cycler with 96-Deep Well Reaction Module Analytik Jena† North America 950030010 International 6321 000.019 Veriti 96-Well Thermal Cycler Thermo Fisher Scientific For select instruments, ramp rates should be...