Library preparation protocol parameters
| Technology | Cell barcode read | Cell barcode offset | Cell barcode length | Input nucleic acid | Library construction method ontology | End bias | Primer | Strand | Umi barcode read | Umi barcode offset | Umi barcode length |
| 10X 3’ v1 | Read 1 / i7 Index | 0 | 14 | polyA RNA | EFO:0009901 | 3 prime tag | poly-dT | first | Read 1 / Read 2 | 14 | 10 |
| 10X 5’ v1 | Read 1 / i7 Index | 0 | 14 | polyA RNA | EFO:0011025 | 5 prime tag | poly-dT | first | Read 1 | 14 | 10 |
| 10X 3’ v2 | Read 1 | 0 | 16 | polyA RNA | EFO:0009899 | 3 prime tag | poly-dT | first | Read 1 | 16 | 10 |
| 10X 5’ v2 | Read 1 | 0 | 16 | polyA RNA | EFO:0009900 | 5 prime tag | poly-dT | first | Read 1 | 16 | 10 |
| 10X 3’ v3 | Read 1 | 0 | 16 | polyA RNA | EFO:0009922 | 3 prime tag | poly-dT | first | Read 1 | 16 | 12 |
| | | | | | | | | | | | |
| inDrop | Read 2 | 0 | 8 | polyA RNA | EFO:0008780 | 3 prime tag | poly-dT | first | Read 2 | 8 | 6 |
| DroNc-seq | Read 1 | 0 | 12 | polyA RNA | EFO:0008720 | 3 prime tag | poly-dT | first | Read 1 | 12 | 8 |
| Drop-seq | Read 1 | 0 | 12 | polyA RNA | EFO:0008722 | 3 prime tag | poly-dT | first | Read 1 | 12 | 8 |
| | | | | | | | | | | | |
| Fluidigm C1-based library preparation | NA | NA | NA | polyA RNA | EFO:0010058 | full length | poly-dT | unstranded | NA | NA | NA |
| Smart-like | NA | NA | NA | polyA RNA | EFO:0010184 | full length | poly-dT | unstranded | NA | NA | |
| Smart-seq | NA | NA | NA | polyA RNA | EFO:0008930 | full length | poly-dT | unstranded | NA | NA | NA |
| Smart-seq2 | NA | NA | NA | polyA RNA | EFO:0008931 | full length | poly-dT | unstranded | NA | NA | NA |
| | | | | | | | | | | | |
| CEL-seq | Read 1 | 0 | 16 | polyA RNA | EFO:0009294 | 3 prime tag | poly-dT | first | Read 1 | 16 | 12 |
| CEL-seq2 | Read 1 | 6 | 6 | polyA RNA | EFO:0010010 | 3 prime tag | poly-dT | first | Read 1 | 0 | 6 |
| | | | | | | | | | | | |
| sci-RNA-seq | Read 1 | 8 | 10 | polyA RNA | EFO:0010550 | 3 prime tag | poly-dT | first | Read 1 | 0 | 8 |
| | | | | | | | | | | | |
| Seq-Well | Read 1 | 0 | 12 | polyA RNA | EFO:0008919 | 3 prime tag | poly-dT | first | Read 1 | 12 | 8 |
| | | | | | | | | | | | |
| 10X scATAC-seq | i5 Index | 0 | 16 | DNA | EFO:0030007 | full length | random | unstranded | NA | NA | NA |
| scATAC-seq (Microfluidics) | i5 Index | 0 | 16 | DNA | EFO:0008904 | full length | random | unstranded | NA | NA | NA |
| | | | | | | | | | | | |
| CITE-seq (cell surface protein profiling) | Read 1 | 0 | 16 | polyA RNA | EFO:0030008 | 3 prime tag | poly-dT | first | Read 1 | 16 | 12 |
| CITE-seq (sample multiplexing) | Read 1 | 0 | 16 | polyA RNA | EFO:0030009 | 3 prime tag | poly-dT | first | Read 1 | 16 | 12 |
| | | | | | | | | | | | |
| ATAC-seq | NA | NA | NA | DNA | DNA library construction (EFO:0010172) | full length | random | unstranded | NA | NA | NA |
| RNA-seq | NA | NA | NA | polyA RNA | cDNA library construction (EFO:0004187) | full length | poly-dT | unstranded | NA | NA | NA |
| | | | | | | | | | | | |
| Visium Spatial Gene Expression | i5 Index & i7 Index | 0 | 10 | polyA RNA | EFO:0010961 | 3 prime tag | poly-dT | first | Read 1 | 0 spatial,16 umi | 16 spatial,10 umi |
Sequencing protocol parameters
| Technology | Paired end | Sequencing method | Sequencing method ontology |
| 10X 3’ v1 | no | tag based single cell RNA sequencing | EFO:0008440 |
| 10X 5’ v1 | no | tag based single cell RNA sequencing | EFO:0008440 |
| 10X 3’ v2 | no | tag based single cell RNA sequencing | EFO:0008440 |
| 10X 5’ v2 | no | tag based single cell RNA sequencing | EFO:0008440 |
| 10X 3’ v3 | no | tag based single cell RNA sequencing | EFO:0008440 |
| | | | |
| inDrop | no | tag based single cell RNA sequencing | EFO:0008440 |
| DroNc-seq | no | tag based single cell RNA sequencing | EFO:0008440 |
| Drop-seq | no | tag based single cell RNA sequencing | EFO:0008440 |
| | | | |
| Fluidigm C1-based library preparation | yes | full length single cell RNA sequencing | EFO:0008441 |
| Smart-like | yes | full length single cell RNA sequencing | EFO:0008441 |
| Smart-seq | yes | full length single cell RNA sequencing | EFO:0008441 |
| Smart-seq2 | yes | full length single cell RNA sequencing | EFO:0008441 |
| | | | |
| CEL-seq | no | tag based single cell RNA sequencing | EFO:0008440 |
| CEL-seq2 | no | tag based single cell RNA sequencing | EFO:0008440 |
| | | | |
| sci-RNA-seq | no | tag based single cell RNA sequencing | EFO:0008440 |
| | | | |
| Seq-Well | no | tag based single cell RNA sequencing | EFO:0008440 |
| | | | |
| 10X scATAC-seq | yes | scATAC-seq | EFO:0010891 |
| scATAC-seq (Microfluidics) | yes | scATAC-seq | EFO:0010891 |
| | | | |
| CITE-seq (cell surface protein profiling) | no | tag based single cell RNA sequencing | EFO:0008440 |
| CITE-seq (sample multiplexing) | no | tag based single cell RNA sequencing | EFO:0008440 |
| | | | |
| ATAC-seq | no | ATAC-seq | EFO:0007045 |
| RNA-Seq | no | RNA-Seq | EFO:0008896 |
| | | | |
| Visium Spatial Gene Expression | no | Visium Spatial Gene Expression | EFO:0010961 |