Question: Can Multiome Single Cell libraries be pooled with other 10x libraries?
Answer: Multiome Gene Expression libraries can be pooled with other dual-indexed gene expression libraries. Multiome ATAC libraries can be pooled with standalone ATAC libraries only on certain Illumina sequencers like MiSeq, HiSeq 2000/2500, NovaSeq 6000 (v1 reagents) sequencers and using 16bp for the i5 read. Although typically, Multiome ATAC libraries are sequenced at i5=24 bp, but when pooled with standalone ATAC libraries (V1, V1.1) on certain Illumina sequencers listed above, they have to be sequenced at i5=16 bp to be compatible with both library structures. Reading past 16 bp on i5 on standalone ATAC libraries could create issues with Cell Ranger ATAC.
There are no disadvantages of sequencing Multiome ATAC libraries with i5=16 bp when sequenced on the sequencers listed above.
Note: We do not recommend pooling Multiome Gene Expression libraries with Multiome ATAC libraries on the same flow cell as they have differing sequencing specifications. Additional information can be found at: Can Multiome ATAC and Multiome GEX libraries be sequenced together?
Products: Single Cell Multiome ATAC + GEX