Sample Index Sets for Single Cell 3'

Specifications, Last Modified on July 7, 2020, Permalink

Dual index plates

Dual index plates are used with Chromium Single Cell 3' 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. Please see our software support site for more information.

Please note that the sample index plate used for 3’ v3.1 Dual Index Gene Expression libraries is different from the sample index plate used for 3’ v3.1 Dual Index Cell Surface Protein and CRISPR Screening libraries.

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

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

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:

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:

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