GSM5811786: 10x of HL60 differentiation, scRNA-seq, 1; Homo sapiens; OTHER
HL60 differentiations were initialized on different days so that all samples could be harvested in a single scRNA-seq reaction to minimize batch effects. Cells were treated with 1 µM ATRA and differentiated for 0 (no ATRA treatment), 1, 2, 3, 4, or 5 days, with all differentiations performed in biological replicates. Samples were tagged or "cell hashed" (Stoeckius et al., 2018) with distinct BD sample tags (BD Bioscience, cat#PN 633780) to enable demultiplexing of cells, and then pooled for scRNA-seq. scRNA-seq was performed on one lane of the 10x Chromium™ Single Cell 3' v2 system following the standard library prep protocol (10x Genomics Single Cell 3' Reagent Kits v2 User Guide, CG00052). Libraries were amplified with 10 cycles of cDNA amplification and 15 cycles of Sample Index PCR. BD Sample Tags were size-separated by SPRI selection after cDNA amplification and amplified according to standard protocols (BD User-Demonstrated Protocol: BD Single-Cell Multiplexing Kit—Human Doc ID: 179682 Rev. 1.0). Final cDNA and sample tag libraries were sequenced on a NovaSeq 6000 (Illumina).