CyTOF data
Description
This dataset includes CyTOF generated single cell proteomics data for AML cells and PDX samples in response to treatment as described below: 1) OCIAML3 cells treated with DMSO (P1) and ERKi (P2) for 24 hours followed by CyTOF. 2) NRAS mutant PDX cells treated with DMSO (PS1), ABT199 (PS2), ERKi (PS3) and Combination (PS4) ex-vivo followed by CyTOF. 3) PDX BM cells from mice treated with Vehicle (c11), ABT199 (c12), ASTX029 (c13) and Combination (c14).
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Steps to reproduce
CyTOF mass cytometry Antibodies other than the Standard BioTools antibodies were conjugated by users or staff in-house at the Flow Cytometry Cellular Imaging Core Facility, North Campus at MD Anderson, according to the Standard BioTools MaxPar Antibody Labeling User Guide, and re-suspended at 0.5 mg/ml in an antibody stabilizer (Candor #131125). The metal content of each conjugated antibody was determined by CyTOF Helios in solution mode against standards (Claritas CLMS-1 ICP-MS Multi-Element Solution). Barcoding and antibody staining: In vitro: OCIAML3 cells were incubated with DMSO control and ERKi for 24 h, and 1.5 million cells were subjected to surface and intracellular staining with metal-conjugated antibodies. Samples were analyzed using a CyTOF mass cytometer fitted with an AS5 autosampler (DVS Sciences). The bead signature was routinely applied to normalize the CyTOF data before analysis. Briefly, viable single cells (cisplatin-low) were gated and analyzed using FlowJo software (v10.7). Ex-vivo: PDX BM cells were treated with DMSO, ABT199, ERKi and combination ex vivo followed by antibody staining and CyTOF. In-vivo: PDX BM cells were isolated from mice treated with vehicle, ABT199, ASTX029, and combination at day 27 of treatment and were stained with metal-tagged antibodies against cell surface markers, barcoded with Fluidigm barcodes, pooled, then stained with metal-tagged antibodies against intracellular proteins and subjected to CyTOF analysis. Human TruStain FcX (BioLegend, #422302) was used to block Fc receptors both prior to and during antibody staining to reduce non-specific binding in experiments involving human AML cells or PDX-derived samples.