Table 4. Top 20 correlations between GFP and LC3.

Top 20 correlations between GFP and LC3 in transfected cells
Plate	Well name	Gene	Median correlation	Standard deviation
As an alternative readout for finding autophagy substrates/triggers we examined GFP/LC3 correlation. Note that p62 appears close to the top of the list, validating the approach (since autophagy adapters are known to be preferred substrates for autophagy, and to recruit LC3 to auto-aggregates).
To control for variation in transfection efficiency between DNA constructs we designed our analysis pipeline to only measure properties of transfected cells exhibiting GFP fluorescence. In this manner we were able to observe genuine signals induced by bacterial protein expression without being swamped by background noise from untransfected cells. The threshold for selecting cells as transfected was determined from samples taken from across untransfected wells, and was designed to use both a median intensity and mean absolute deviation intensity, to avoid under-selection of cells with either diffuse, or highly punctate signals. By this measure transfection efficiency ranged between 40-60% for LF82 genes, and 60% for empty pCMV-mEm-4GS vector. An average of 183 cells were present per site, with 90 successfully transfected cells for LF82 genes and 112 successfully transfected cells for control well sites.
Set1_Part1	C09	LF82_153	2.93	1.15
Set1_Part1	C08	LF82_152	2.75	1.51
Set3_Part2	F08	LF82_266	2.63	1.03
Set3_Part2	G09	p62	2.61	0.80
Set1_Part1	E05	LF82_326	2.57	1.44
Set3_Part2	C05	LF82_758	2.53	1.26
Set3_Part2	E08	LF82_121	2.50	1.12
Set1_Part1	E06	LF82_327	2.46	1.83
Set1_Part1	D09	LF82_250	2.44	1.61
Set1_Part1	E04	LF82_325	2.40	1.49
Set1_Part1	F11	LF82_603	2.27	1.47
Set1_Part1	B08	LF82_091	2.19	1.54
Set1_Part1	D08	LF82_248	2.13	1.47
Set1_Part1	E09	LF82_355	2.07	1.54
Set1_Part1	F07	LF82_537	2.05	1.50
Set3_Part2	C06	LF82_109	2.04	1.39
Set1_Part1	E07	LF82_350	2.01	1.34
Set3_Part2	D05	LF82_336	1.99	0.89
Set3_Part2	D04	LF82_0556	1.94	1.44
Set1_Part1	F02	LF82_434	1.94	1.53
Set1_Part1	E08	LF82_353	1.94	1.29