10x Genomics Support/Single Cell Immune Profiling/Documentation/Library Construction/

Sample Index Sets for Single Cell Immune Profiling

Dual index plates

Dual index plates are used with Chromium Single Cell 5' v3, 5' v2, and 5' HT v2 Dual Index libraries.

Each well of a dual index plate contains a mix of one unique i7 and one unique i5 sample index.

The files below contain the mappings from the sample index names to the associated set of Index (i7) and Index 2 (i5) oligonucleotides. Both the forward and reverse complement sequences are listed for the i5 sequence. Please see this article for more information.

Different index plates are required for different 5’ v3 and 5' v2 Dual Index library types. Always make sure to select the correct sample index plate for the appropriate library type.

5' v3, 5' v2, and 5' HT v2 Dual Index Gene Expression, V(D)J, and CRISPR libraries are made using the following sample index plate:

  • PN-1000215: Dual Index Kit TT, Set A: CSV | JSON

5' v3, 5’ v2, and 5' HT v2 Dual Index Cell Surface Protein libraries are made using the following sample index plate:

  • PN-1000250: Dual Index Kit TN, Set A: CSV | JSON

5’ v2 Dual Index Barcode Enabled Antigen Mapping (BEAM)* libraries are made using the following sample index plate:

  • PN-1000251: Dual Index Kit TS, Set A: CSV | JSON

*Feature Barcode technology for BEAM is not supported with the Single Cell Immune Cell Profiling 5' v3 assay

Single index plates

Single index plates are used with Chromium Single Cell 5' v1 and v1.1 libraries.

Sample indexes for use with the Chromium Single Cell 5' v1 and v1.1 reagent kits each comprise four oligonucleotides. When analyzing sequencing data for a given sample, you must combine the reads associated with all four of the oligonucleotides in the sample index.

Please note that the sample index plate used for V(D)J Enriched and 5’ Gene Expression libraries are different from the sample index plate used for 5' Cell Surface Protein and Antigen Specificity libraries.

5' v1.1 Gene Expression and V(D)J enriched libraries are made using the following sample index plate:

  • PN-1000213: Single Index Kit T Set A: CSV | JSON

5' v1.1 Cell Surface Protein and Antigen Specificity libraries are made using the following sample index plate:

  • PN-1000212 Single Index Kit N Set A: CSV | JSON
Document Type
Specifications

Last Modified
March 15, 2023