Sample Prep - Nuclei

• How can I optimize my nuclei prep for Single Cell ATAC sequencing?
• How can I assess the quality of my nuclei for Single Cell ATAC Sequencing?
• Can I run samples with low cell viability?
• I want to perform both Single Cell ATAC and Gene Expression profiling, which sample preparation protocol should I use?
• Do I need to dissociate tissues into single cells first before isolating nuclei, or can I use the whole tissue?
• Why is using diluted Nuclei Buffer for resuspending my nuclei important?

Transposition

• Can whole cells be used as input into the transposition reaction?

Sequencing

• Can Single Cell ATAC libraries be pooled with non-ATAC libraries for sequencing?

Software

• How can I convert the peak-barcode matrix from Cell Ranger ATAC 1.x to a CSV file?
• How do I calculate median number of peaks per cell for Cell Ranger ATAC?
• How can I compare scATAC and scRNA-seq data from the same biological sample?
• Does the Cell Ranger ATAC pipeline use static thresholds to call peaks and identify cell barcodes?
• How can I compare results from multiple Cell Ranger ATAC v1.0 runs?
• What annotations are included in the downloadable reference genomes for Cell Ranger ATAC?

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