Potential Inconsistency in Platemap for Batch 1 (20X)

[gwaybio]

Hi @mekelley and @ayberman,

I am working through implementing a PSMB5 signature analysis (described briefly here https://github.com/broadinstitute/profiling-resistance-mechanisms/issues/49#issuecomment-597829046)

This requires using data from early batches (batch 1 20x and batch 2). These are the only batches to have profiles for clones A and E (the only confirmed PSMB5 mutations), correct?

I noticed that there is a bit of a wonky platemap:

Copy and pasted below:

plate_map_name	well_position	CellLine	Dosage
PlateMap_HCT116bortezomib	B03	WT	0
PlateMap_HCT116bortezomib	B04	WT	0
PlateMap_HCT116bortezomib	B05	WT	0
PlateMap_HCT116bortezomib	B06	CloneA	0
PlateMap_HCT116bortezomib	B07	CloneA	0
PlateMap_HCT116bortezomib	B08	CloneA	0
PlateMap_HCT116bortezomib	B09	CloneE	0
PlateMap_HCT116bortezomib	B10	CloneE	0
PlateMap_HCT116bortezomib	B11	CloneE	0
PlateMap_HCT116bortezomib	C03	WT	0.7
PlateMap_HCT116bortezomib	C04	WT	0.7
PlateMap_HCT116bortezomib	C05	WT	0.7
PlateMap_HCT116bortezomib	C06	CloneA	0.7
PlateMap_HCT116bortezomib	C07	CloneA	0.7
*PlateMap_HCT116bortezomib	F08	CloneA	0.7
PlateMap_HCT116bortezomib	C09	CloneE	0.7
PlateMap_HCT116bortezomib	C10	CloneE	0.7
PlateMap_HCT116bortezomib	C11	CloneE	0.7
PlateMap_HCT116bortezomib	D03	WT	7
PlateMap_HCT116bortezomib	D04	WT	7
PlateMap_HCT116bortezomib	D05	WT	7
PlateMap_HCT116bortezomib	D06	CloneA	7
PlateMap_HCT116bortezomib	D07	CloneA	7
PlateMap_HCT116bortezomib	D08	CloneA	7
PlateMap_HCT116bortezomib	D09	CloneE	7
PlateMap_HCT116bortezomib	D10	CloneE	7
PlateMap_HCT116bortezomib	D11	CloneE	7
PlateMap_HCT116bortezomib	E03	WT	70
PlateMap_HCT116bortezomib	E04	WT	70
PlateMap_HCT116bortezomib	E05	WT	70
PlateMap_HCT116bortezomib	E06	CloneA	70
PlateMap_HCT116bortezomib	E07	CloneA	70
PlateMap_HCT116bortezomib	E08	CloneA	70
PlateMap_HCT116bortezomib	E09	CloneE	70
PlateMap_HCT116bortezomib	E10	CloneE	70
PlateMap_HCT116bortezomib	E11	CloneE	70

This doesn't impact analysis much at all, just confirming that the F above should be a C. Also, on the chance that this is indeed a small mistake - this stuff happens literally all the time, so no worries! 😹 It is good to confirm and clear up once identified. ( I didn't catch it in my original processing!)

[ayberman]

Hey Greg,

Regarding your questions about the plate map for 2-15-19, the well is indeed 8F. I accidentally plated the cells incorrectly in well C, so I replated that condition in well F.

As for the batches, I'm pretty sure those are the only batches, but hopefully Megan can confirm?

[gwaybio]

I accidentally plated the cells incorrectly in well C, so I replated that condition in well F.

Got it - thanks for the quick confirmation