K562 cells were transduced with a pool containing 18 total sgRNAs (8 sgRNAs targeting 4 different genes and 10 non-targeting control sgRNAs). JK562 dCas9 parental cells were transduced and selected cells (cultured in a selection media) were frozen. Aliquots were thawed, counted, and loaded onto the Chromium X.
Approximately 16,000 cells were loaded (7,632 cells recovered). Libraries were generated as described in the Chromium Single Cell 5' Reagent Kits User Guide (v2 Chemistry Dual Index) (CG000331 Rev C) using the Chromium Controller. Libraries were sequenced on an Illumina NovaSeq 6000 to a read depth of approximately 40,000 mean reads per cell for Gene Expression libraries and 5,000 mean reads per cell for CRISPR screening libraries.
Paired-end, dual indexing:
- Read 1: 26 cycles (16 bp barcode, 10 bp UMI)
- i5 index: 10 cycles (sample index)
- i7 index: 10 cycles (sample index)
- Read 2: 90 cycles (transcript)
Analysis parameters used: --expect-cells= 10000