Sample Indices
Each sample index in the Dual Index Kit TS Set A (PN-1000251), Dual Index Kit TN Set A (PN-1000250), and Dual Index Kit TT Set A (PN-1000215) 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 (e.g. 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.
Optimal demultiplexing depends on library loading concentration, quality, quantification, pooling ratios, and other factors such as color balance in the index read. For more details, especially when sequencing low-plex pools, see:
- What index combinations should I select when sequencing low plex pools of 10x Genomics libraries on Illumina sequencers?
- What considerations are there for sequencing low plex pools of 10x Genomics libraries on Illumina sequencers?
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 Gene Expression is different from the sample index plates used for Flex Protein Expression or Flex CRISPR.
Flex Gene Expression libraries libraries are made using the following sample index plate:
Flex Protein libraries are made using the following sample index plate:
Flex CRISPR and Next GEM Flex Protein libraries (using TotalSeq™️-B) are made using the following sample index plate: