GSM8721081: Parse whole-transcriptome single-cell RNA-seq for all HCC1806 and MDA-MB-231 samples; Homo sapiens; RNA-Seq
Single-cell RNA preparation was performed according to manufacturer guidelines from Parse outlined in CRISPR Detect for Evercode WT v2 (User Manual Version 1.1, UM0025). Library prep was performed according to manufacturer guidelines from Parse outlined in CRISPR Detect for Evercode WT v2 (User Manual Version 1.1, UM0025). As the WT kit can process 100,000 cells, samples from both cell lines were prepared with the same kit. For each cell line, the 'initial' sample was split over 4 wells targeting 13,000 cells total, each of the four 'pre-sort' samples were split over 3 wells targeting 6,250 cells per sample, and each of the sorted control and fusion-enriched samples received its own well, targeting 1500 cells per sample. 8 identical sublibraries were prepared, but one sublibrary (sublibrary 5) was lost during preparation, adjusting the expected cell number to 87,500 total and 11,375, 5,469, and 1312 per sample per cell line, respectively. ClonMapper Duo gRNA barcodes were amplified from sublibrary cDNA according to manufacture instructions for CRISPR Sequencing Library Preparation in CRISPR Detect for Evercode WT v2 (User Manual Version 1.1, UM0025). Whole transcriptome and CRISPR detect (CMDuo barcode) libraries were amplified separately from cDNA and sequenced independently across 8 sublibraries each. Whole transcriptome and CRISPR Detect sublibraries were sequenced at the UT Austin Genomic Sequencing and Analysis on a NovaSeq 6000 (S2 flow cell, paired-end, 200 cycles). 500e6 reads were targeted for each WT sublibrary and 50e6 reads for each CRIPSR Detect sublibrary, producing 41,973 mean reads per cell across transcriptomic libraries and 3,238 means reads per cell in the combined CRISPR Detect sublibraries.