Question: What oligos are in my sample index?
Answer: This depends on whether the libraries were generated with a single sample index (i7) or dual sample indexes (i5 and i7).
Dual index sample index plates: Each well is a mix of 2 oligonucleotides, one of which contains a unique i7 sample index and one of which contains a unique i5 sample index.
Single index sample index plates: Each well is a mix of 4 oligonucleotides, each of which contains a unique i7 sample index. Using 4 oligos per sample index ensures that the i7 index read is balanced across all 4 bases during sequencing.
Each sample index in each of the 96-well sample index plates is unique. When pooling libraries for sequencing on the same lane of a flowcell, ensure that each library is generated using a different sample index. The 10x sample index name is not needed for setting up an Illumina run but is needed for demultiplexing sequencing runs when running more than one sample per lane. See: Is a sample sheet required for sequencing?
The sample index sequences can be found here:
- Visium Spatial Gene Expression Libraries
- Visium Spatial Gene Expression for FFPE Libraries
- Single Cell 3' Libraries
- Single Cell Immune Profiling Libraries
- Single Cell ATAC Libraries
- Single Cell Multiome ATAC + GEX libraries
- Fixed RNA Profiling
- Genome/Exome Libraires
- Single Cell DNA