Question: Which region should I select when determining the average fragment size of my library?
Answer: The table below shows the appropriate region to select for each library type. For example, for a Single Cell 3’ Gene Expression library, select the region from 200 bp to 2,000 bp when determining the average fragment size on the BioAnalyzer, TapeStation or LabChip. The average fragment size is needed for the size adjustment calculation when quantifying libraries using the qPCR-based KAPA Library Quantification Kit.
|
Library type |
Region selection (bp) |
| Chromium Single Cell 3' Gene Expression | 200-2,000 |
| Chromium Single Cell 3' Cell Surface Protein | 150-300 |
| Chromium Single Cell 3' CRISPR Screening | 200-400 |
| Chromium Single Cell 3' CellPlex | 150-300 |
| Chromium Single Cell 5' Gene Expression | 200-2,000 |
| Chromium Single Cell 5' V(D)J | 200-2,000 |
| Chromium Single Cell 5' Cell Surface Protein | 150-300 |
| Chromium Single Cell 5' CRISPR Screening | 200-400 |
| Chromium Single Cell 5' Barcode Enabled Antigen Mapping (BEAM) | 150-300 |
| Chromium Single Cell ATAC | 175-1,000 |
| Chromium Single Cell Multiome ATAC | 175-1,000 |
| Chromium Single Cell Multiome Gene Expression | 200-2,000 |
| Chromium Fixed RNA Profiling - Gene Expression | 150-300 |
| Chromium Fixed RNA Profiling - Cell Surface Protein | 150-300 |
| Visium Spatial Gene Expression (Fresh Frozen) | 200-2,000 |
| Visium Spatial Gene Expression for FFPE | 150-300 |
| Visium CytAssist Spatial Gene Expression (FFPE, Fresh Frozen, Fixed Frozen) | 150-300 |
| Visium CytAssist Spatial Gene & Protein Expression (FFPE) | 150-300 |
Also see:
How do I determine the average fragment size of a Single Cell ATAC or Multiome ATAC final library?
Products: Single Cell Gene Expression, Single Cell Immune Profiling, Single Cell Gene Expression Flex, Fixed RNA Profiling, Single Cell Multiome ATAC + GEX, Single Cell ATAC, Visium for Fresh Frozen, Visium for FFPE, Visium CytAssist for FFPE, Visium CytAssist for FF, Visium CytAssist for FxF, Visium CytAssist Gene and Protein