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Sample Index Sets for Single Cell 3'

Dual index plates

Dual index plates are used with Chromium Single Cell 3' v3.1, 3' LT v3.1, and 3' HT v3.1 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 and our software support site for more information.

Please note that the sample index plate used for 3’ v3.1 and LT v3.1 Dual Index Gene Expression libraries is different from the sample index plates used for 3’ v3.1 and LT v3.1 Dual Index Feature Barcode libraries.

3’ v3.1 and LT v3.1 Dual Index Gene Expression libraries are made using the following sample index plate:

  • PN-1000215/PN-3000431: Dual Index Kit TT, Set A: CSV | JSON

3’ v3.1/LT v3.1* Dual Index Cell Surface Protein and 3' v3.1 CRISPR Screening libraries are made using the following sample index plate:

  • PN-1000242/PN-3000483: Dual Index Kit NT, Set A: CSV | JSON

3’ v3.1 Dual Index Cell Multiplexing libraries are made using the following sample index plate:

  • PN-1000243/PN-3000482: Dual Index Kit NN, Set A: CSV | JSON

* Only Feature Barcode technology for Cell Surface Proteins is supported with the Single Cell 3' LT v3.1 assay. Feature Barcode technology for CRISPR screening is not supported with the Single Cell 3' LT v3.1 assay.

Single index plates

Single index plates are used with Chromium Single Cell 3' v3.1 (Single Index), v3 and v2 libraries.

Each well of a single index plate comprises 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.

The files below contain the mappings from the sample index names to the associated set of four oligonucleotides.

Chromium Single Cell v3.1 uses the following i7 sample index set:

  • PN-1000213/PN-2000240: Single Index Kit T Set A: CSV | JSON

Chromium Single Cell (v2 and v3) share the same i7 sample index set:

  • PN-120262/PN-220103: Chromium i7 Multiplex Kit: CSV | JSON
Document Type
Specifications

Last Modified
June 13, 2022