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source_pdf: 10xChromium3v4.pdf |
source_path: /Users/seqmachines/playground/protocols-test/scg-v1-upload/protocols/10x_chromium_3_gene_expression_v4/10xChromium3v4.pdf |
extraction: Docling: PdfPipelineOptions(do_ocr=False); assembled markdown plus Docling native PDF layout prediction text cells sorted by page/y/x |
## Docling assembled markdown |
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## User Guide | CG000731 | Rev B |
## Chromium GEM-X Single Cell 3' Reagent Kits v4 |
## For use with: |
Chromium GEM-X Single Cell 3' Kit v4 16 rxns PN-1000691 | 4 rxns PN-1000686 |
Chromium GEM-X Single Cell 3' Chip Kit v4 4 chips PN-1000690 |
Dual Index Kit TT Set A 96 rxns PN-1000215 |
## Notices |
## Document Number |
CG000731 | Rev B |
## Legal Notices |
© 2024 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 product. 10x Genomics provides no warranty and hereby disclaims any and all warranties as to the |
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 accompanying the purchase of such use of any third-party products o... |
## Instrument & Licensed Software Updates Warranties |
Updates to existing Instruments and Licensed Software may be required to enable customers to use new or existing products. In the event of an Instrument failure resulting from an update, such failed Instrument will be replaced or repaired in accordance with the 10x Limited Warranty, Assurance Plan or service agreement,... |
## Support |
Email: support@10xgenomics.com 10x Genomics 6230 Stoneridge Mall Road Pleasanton, CA |
## Document Revision Summary |
## Document Number |
CG000731 | Rev B |
## Title |
Chromium GEM-X Single Cell 3' Reagent Kits v4 |
## Revision |
Rev A to Rev B |
## Revision Date |
August 29, 2024 |
## Description of Changes |
- l Updated for general minor consistency of language and terms throughout |
- l Updated at multiple instances throughout: |
- o Chromium X/iX instrument to Chromium X Series instrument |
- o Chromium X/iX Chip Holder to Chromium X Series Chip Holder |
- o Chromium X Series Accessory Kit name and part number No change in functionality |
- l Updated firmware version note in Tips & Best Practices section (page 23) and in Run the Chromium X Series Instrument section (page 38) |
## Table of Contents |
| Introduction | | |
|------------------------------------------------------------------------------|----| |
| Chromium GEM-X Single Cell 3' Reagent Kits v4 | 7 | |
| 10x Genomics Accessories | 10 | |
| Third-Party Items | 10 | |
| Protocol Steps & Timing | 11 | |
| Stepwise Objectives | 12 | |
| Tips & Best Practices | | |
| Step 1: GEM Generation and Barcoding | | |
| 1.0 Get Started | 30 | |
| 1.1 Prepare Master Mix | 31 | |
| Assemble GEM-X Chip | 32 | |
| 1.2 Load GEM-X Chip | 36 | |
| 1.3 Run the Chromium X Series Instrument | 38 | |
| 1.4 Transfer GEMs | 39 | |
| 1.5 GEM-RT Incubation | 40 | |
| Step 2: Post GEM-RT Cleanup & cDNA Amplification | | |
| 2.0 Get Started | 42 | |
| 2.1 Post GEM-RT Cleanup - Dynabeads | 43 | |
| 2.2 cDNA Amplification | 46 | |
| 2.3 cDNA Cleanup - SPRIselect | 47 | |
| 2.4 Post cDNA Amplification QC & Quantification | 48 | |
| Step 3: 3' Gene Expression Library Construction | | |
| 3.0 Get Started | 51 | |
| Step Overview (Step 3.1d) | 52 | |
| 3.1 GEX Fragmentation, End Repair & A-tailing | 53 | |
| 3.2 GEX Post Fragmentation, End Repair & A-tailing Double Sided - SPRIselect | 55 | |
| 3.3 GEX Adaptor Ligation | 56 | |
| 3.4 GEX Post Ligation Cleanup - SPRIselect | 57 | |
| 3.5 GEX Sample Index PCR | 58 | |
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