Sample Prep - Cells

• Which 10x Demonstrated Protocols are compatible with the Single Cell DNA workflow?
• Are magnetic bead-enriched cells compatible with Single Cell DNA?
• Can BSA be substituted with another serum in the cell suspension buffer?
• Are fluorescent DNA stains compatible with Single Cell DNA analysis?
• Do my cells need to be viable for Single Cell DNA analysis?
• What alternative cell suspension buffers can be used?

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Cell Bead Generation and Processing

• What percentage of cells are encapsulated in Cell Beads?
• Can I leave Cell Beads shaking longer than 24 hours?
• How large are Cell Beads?
• Why are Cell Beads necessary?

GEM Generation and Barcoding

• How much of a single cell's genome is amplified?
• How are the 10x Barcodes added to the amplified DNA?
• How is genomic DNA amplified in the Single Cell DNA workflow?
• What if I don't have enough Cell Beads to load onto Chip D?

Post GEM Incubation Cleanup & QC

• What is the expected DNA yield after GEM isothermal reaction?

Library Construction

• What is the expected size range of the final Single Cell DNA library?

Sequencing

• What is the recommended sequencing depth for non-human experiments?

Software

• Does Cellranger DNA support multi-species (barnyard) experiments?
• Does Cell Ranger DNA support non-human genomes?
• When does Cell Ranger DNA trigger alerts?
• Does Cell Ranger DNA match and trim barcodes like Long Ranger or Cell Ranger?
• Is a custom Cell Ranger DNA reference required for cells with a baseline ploidy other than 2?
• What are the GP, MP, and DC tags in the Cell Ranger DNA BAM file used for?

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