Question: What oligos are in my sample index?
Answer: Each well in the sample index plate is a mix of 4 unique oligonucleotides. We pool four oligos per sample index so that the i7 index read is balanced across all 4 bases during sequencing.
Each sample index in the 96-well plate is unique, and the sample indexes can be used in any combination. Thus, as long as you choose one unique sample index (a unique well in the 96-well plate) for each of the samples that will be multiplexed, the samples can be run on a single lane of a flow cell.
The sample index sequences can be found here:
- For Genome/Exome Libraries: https://support.10xgenomics.com/genome-exome/index/doc/specifications-sample-index-sets-for-genome-and-exome
- For Single Cell 3' Libraries: https://support.10xgenomics.com/single-cell-gene-expression/index/doc/specifications-sample-index-sets-for-single-cell-3
- For Single Cell V(D)J Libraries: https://support.10xgenomics.com/single-cell-vdj/sequencing/doc/specifications-sample-index-sets-for-single-cell-vdj
- For Single Cell ATAC Libraries: https://support.10xgenomics.com/single-cell-atac/sequencing/doc/specifications-sample-index-sets-for-single-cell-atac
Note: The 10x Sample Index sequence is not needed when setting up the sample sheet, but the 10x Sample Index name is needed for demultiplexing sequencing runs when running more than one sample per lane. For help generating sample sheets, see https://support.10xgenomics.com/genome-exome/software/pipelines/latest/using/bcl2fastq-direct