GSM4008104: Mammary epithelial cell, U72_G12; Homo sapiens; ATAC-seq
Single-cell ATAC-seq libraries were prepared on a Fluidigm C1 instrument using 'ATAC Seq- Cell Load and Stain Rev C' script. Cells were passed through a 20 μm cell strainer (CellTrics, Sysmex Partac) to remove debris and cell aggregates, and mixed at a ratio of 7:3 with C1 suspension reagent. The resulting single-cell suspension was loaded on C1 Single-Cell Open App IFC chip (1862x, 10-17 μm, Fluidigm) at a concentration of 350 cells/μL. Captured cells were stained with 2 μM green-fluorescent calcein-AM and 4 μM red-fluorescent ethidium homodimer-1 (Molecular Probes) and visualized under an EVOS FL cell imaging station (Life Technologies) to ensure successful capture and to determine cell viability. After cell lysis and Tn5 transposition, 8 cycles of pre-amplification were run on IFC chip. Pre-amplified PCR products were transferred to 96-well plates and further amplified for an additional 13 cycles using custom Nextera dual-index primers and NEBNext High-Fidelity 2X PCR master mix (New England Biolabs). Individually barcoded libraries were pooled and purified on a single MinElute column (Qiagen). The quality and size distribution of pooled libraries were evaluated on an Agilent 2100 Bioanalyzer using High Sensitivity DNA reagents (Agilent). Single-cell assay for transposase accessible chromatin followed by sequencing (scATAC-seq)