MEP-LINCS MCF10A_SS1 Cell-Level QA Report

date: 2017-07-26

Summary

This report covers the cell-level data for the MCF10A_SS1 dataset. There are additional reports for the spot and MEP QA and the analysis of this staining set.

Introduction

The LINCS MCF10A_SS1 experiment was performed with MCF10A cells grown in 8 8-well plates. The channels are DAPI, 488, 555, 647, and 750. The endpoints are DAPI, phalloidin, CellMask, mitoTracker, and NA. Color images of the cells at each spot were gathered on a Nikon automated microscope.

The histograms and scatterplots that display cell level data are from a randomly sampled subset of the full dataset.


DAPI QA

Histograms of the total DAPI signal are typicaly bimodal with peaks at the 2N and 4N DNA positions. If the DAPI signal passed the QA test, a blue vertical line shows the gate value for classifying 2N and 4N populations.

For DAPI signals that have been gated, we want to normalize the DNA signal so that the G0/G1 peak has a value of 1. This should yield G2 peak at 2. To achieve this, the total DAPI intensity is divided by the median total DAPI intensity for all cells that have a DNA Cycle State value of 1 (to the left of the blue line).

The plots below are of a randomly sampled subset of the cell-level data.



MitoTracker Analysis

This staining set includes MitoTracker which stains mitochondria.







Supplemental Material