Development of 1-tube EpiTOF panel

This CyTOF/mass cytometry dataset summarizes the development of a 1-tube EpiTOF panel.  This compiles Methylation and Acetylation markers into a single panel, rather than 2 panels as in FR-FCM-Z8FS and FR-FCM-Z8GB on FlowRepository.

Other differences relative to FR datasets:

Addition of more surface markers

Revision of gating pathway

Reduction of Panel 1 and Panel 2 into a single intracellular panel, due to partial redundancy of certain markers, as determined by the Khatri and Utz labs (https://doi.org/10.1101/2022.01.21.477300 and https://doi.org/10.1016/j.isci.2022.105756)

Frozen surface cocktail - more consistent staining between plates/batches

Intracellular cocktail:  roughly half the markers frozen (more consistent staining between plates/batches), roughly half needed to be added as liquid reagents (did not perform well when also frozen)

FBS/DMSO -80C freezing of fully stained (including Ir) samples allowed more samples or plates per staining Batch, increasing throughput

Trial 11 and 11b finish the development work.  Trial 14, 15, and 15B are the final cocktail prep testing for antibody stocks for a Gates Foundation project.

All donors included in testing files are healthy donor PBMCs, processed from LRS chambers from the Stanford Blood Center.  The files were acquired on a Helios mass cytometer (Standard BioTools), normalized using the CyTOF software and the included EQ4 beads (then concatenated if necessary), then debarcoded using the CyTOF software (20plex Pd barcoding kit as in the included staining protocol).  Only the Normalized (concatenated) Debarcoded files are included in this dataset.

Grant ID:  INV-008378

Funding Source:  Bill and Melinda Gates Foundation

We also acknowledge the Purvesh Khatri Lab and PJ Utz Lab (both Stanford University) for initial development.