Question: What barcodes are used in the analysis of 3' and 5' GEM-X Universal Multiplex (a.k.a On-Chip Multiplexing) ?
Answer:
Barcodes used in 3' and 5' On-Chip Multiplexing (OCM) is the same as in GEM-X Universal assays (i.e. ~3.6 million), for both 3’ and 5’ assays. However, the way these barcodes are utilized in analysis differs, as explained below:
- Each OCM barcode (i.e. OB1, OB2, OB3 and OB4), consists of 921,600 distinct barcodes per Gel Bead.
- Chemistry detection relies on the entire 3.6 million Barcode inclusion list, which is the same as GEM-X Universal.
- Sample multiplexing is based on the distinct subset of barcodes assigned to each OCM Barcode (OB), defined in the multi config CSV file of the cellranger multi pipeline.
- Cell Ranger v9.0 and above is used to process OCM data and multi pipeline is used. Please find more information on the analysis here: https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-3p-multi#ocm
Please find below attached OCM barcode lists for the 3' and 5' libraries, along with their respective filenames.
3' OCM barcodes:
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OB1_3M-3pgex-may-2023.txt
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OB2_3M-3pgex-may-2023.txt
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OB3_3M-3pgex-may-2023.txt
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OB4_3M-3pgex-may-2023.txt
5' OCM barcodes:
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OB1_3M-5pgex-jan-2023.txt
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OB2_3M-5pgex-jan-2023.txt
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OB3_3M-5pgex-jan-2023.txt
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OB4_3M-5pgex-jan-2023.txt
- Disclaimer: 10x Genomics does not guarantee or support using the barcode lists with 3rd party tools.
Products: Universal 3' Gene Expression, Universal 5' Gene Expression
Last Updated: March, 2025