Question: What considerations are there for sequencing 10x Genomics libraries on NextSeq 1000/2000 Sequencing Systems with XLEAP SBS kits?
Answer: NextSeq 1000/2000 instruments using the XLEAP SBS chemistry kits have been tested for compatibility for sequencing 10x Genomics libraries in the table below. The table lists the loading concentration and % PhiX input used for 10x Genomics testing.
NextSeq 1000/2000 with XLEAP SBS kits loading guidance
| Product | Library Type | Sequencing Configuration (R1, i7, i5, R2) | Library loading concentration | %PhiX input |
| Chromium Single Cell 3’v4 Dual Index (GEM-X) | Gene Expression | 28, 10, 10, 90 | 650 pM | 1% |
| FB - Cell Surface Protein | ||||
| Chromium Single Cell 3' v3.1, 3' HT Dual index (Next GEM) | Gene Expression | 28, 10, 10, 90 | 650 pM | 1% |
| FB - Cell Surface Protein | ||||
| FB - CRISPR | ||||
| FB - CellPlex | ||||
| Chromium Single Cell 5’v3 Dual Index (GEM-X) | Gene Expression | 28, 10, 10, 90 | 650 pM | 1% |
| V(D)J | ||||
| FB - Cell Surface Protein | ||||
| FB - CRISPR | ||||
| ChromiumSingle Cell 5' v2, 5' HT Dual index (Next GEM) | Gene Expression | 26, 10, 10, 90 | 650 pM | 1% |
| V(D)J | ||||
| FB - Cell Surface Protein | ||||
| FB - CRISPR | ||||
| Chromium Single Cell Gene Expression Flex, singleplex | Gene Expression | 28, 10, 10, 90 | 650 pM | 1% |
| FB - Cell Surface Protein | ||||
| Chromium Single Cell Gene Expression Flex, multiplex | Gene Expression | 28, 10, 10, 90 | 650 pM | 5% |
| FB - Cell Surface Protein | ||||
| Chromium Single Cell Multiome ATAC + Gene Expression | Multiome Gene Expression | 28, 10, 10, 90 | 650 pM | 1% |
| Multiome ATAC | 50, 8, 24, 49 | 650 pM | ||
| Chromium Single Cell ATAC v2 | ATAC | 50, 8, 16, 49 | 650 pM | 1% |
| Visium CytAssist Spatial Gene Expression (V2) | Gene Expression | 28, 10, 10, 50 | 650 pM | 1% |
| Protein | ||||
| Visium HD Spatial Gene Expression | Gene Expression | 43, 10, 10, 50 | 650 pM | 1% |
| Spatial Gene Expression for Fresh Frozen | Gene Expression | 28, 10, 10, 90 | 650 pM | 1% |
Illumina resources
- NextSeq 1000/2000 Specifications Sheet
- NextSeq 1000/2000 XLEAP-SBS and Standard SBS Concordance Tech Note
- Single-cell and spatial sequencing on NextSeq™ 1000 and NextSeq 2000 XLEAP-SBS™ flow cells Tech Note
- Illumina has published run data for sequencing runs on NextSeq 1000/2000 with XLEAP SBS chemistry using 10x Genomics 3’v3.1 Gene Expression Libraries:
- 10x Genomics 3’Gene Expression available on Basespace Sequence Hub
- NextSeq 1000/2000 XLEAP-SBS (P3): 10x Genomics Chromium 3’ Gene Expression libraries
- NextSeq 1000/2000 XLEAP-SBS (P4): 10x Genomics Chromium 3’ Gene Expression libraries
Products: Single Cell Gene Expression, Single Cell Immune Profiling, Single Cell Gene Expression Flex, Single Cell ATAC, Single Cell Multiome ATAC + GEX, Visium for Fresh Frozen, Visium CytAssist for FFPE, Visium HD