Sample Indices

Each sample index in the Dual Index Kit TS Set A (PN-1000251) or Dual Index Kit TN Set A (PN-1000250) is a mix of one unique i7 and one unique i5 sample index. If multiple samples are pooled in a flow cell lane, the sample index name (i.e. the Dual Index TS Set A plate well ID, SI-TS-) is needed in the sample sheet used for generating FASTQs with “cellranger mkfastq”. Samples utilizing the same sample index should not be pooled together, or run on the same flow cell lane, as this would not enable correct sample demultiplexing.

Color balance in the index read is important for optimal quality and demultiplexing results. For example, when pooling samples on the NovaSeq X Series instruments, Illumina recommends avoiding index combinations which only have signals from A bases, G bases, or G+A bases in any given cycle. Refer to Illumina’s guidance on index color balancing.

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 Flex is different from the sample index plates used for Flex.

Flex Gene Expression libraries libraries are made using the following sample index plate:

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

In the tables below are suggested index combinations when sequencing low-plex pools on 2-channel systems. The following criteria were used for selecting these index combinations:

• For 2-channel systems with XLEAP-SBS chemistry (e.g. NovaSeq X Series, NextSeq 1000/2000 XLEAP-SBS), each cycle of the index read should contain at least one C or T. This follows Illumina's guidance to avoid index combinations that have signal in the blue channel only (from A or A+G) or no signal (only G)
• For 2-channel systems with non-XLEAP SBS chemistry (e.g. NovaSeq 6000, NextSeq 2000 standard SBS), each cycle of the index read should contain at least one non-G base. This follows Illumina's guidance of selecting index combinations that provide signal in at least one channel, preferably both channels (blue channel - A or C; green channel - A or T)

These index combinations are suggested theoretical combinations to optimize color balance. Not all index combinations have been specifically tested. 10x Genomics has not performed extensive testing of low plex pools.

The tables below are not exhaustive and may not cover all possible index combinations from Dual Index Plate TS Set A.

Flex Protein libraries are made using the following sample index plate:

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

Next GEM Flex Protein libraries (using TotalSeq™️-B) are made using the following sample index plate:

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