Batch 9 and 10 Data Summary

[gwaybio]

We added Batch 9 (2020_08_24_Batch9) and Batch 10 (2020_09_09_Batch10) profiles in #85 and audited in #88. I describe them in more detail below:

Including the data described in #40, we now have a total of 1,713 profiles

Split by batch:

Plate Contents

Batch 9 (2020_08_24_Batch9)

Click to expand plate contents [6 plates]

• 6 plates
  • 218775
    • Treatment: CB-5083 (700 nM)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, CB5038 clone 17, CB5038 clone 16, CB5038 clone 15, CB5038 clone 14, CB5038 clone 13
  • 218774
    • Treatment: DMSO (0.1%)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, CB5038 clone 17, CB5038 clone 16, CB5038 clone 15, CB5038 clone 14, CB5038 clone 13
  • 218699
    • Treatment: Ixazomib (50 nM)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, Ixazomib clone 01, Ixazomib clone 02, Ixazomib clone 03, Ixazomib clone 04, Ixazomib clone 05
  • 218698
    • Treatment: DMSO (0.1%)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, Ixazomib clone 01, Ixazomib clone 02, Ixazomib clone 03, Ixazomib clone 04, Ixazomib clone 05
  • 218697
    • Treatment: CB-5083 (700 nM)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, CB5038 clone 17, CB5038 clone 16, CB5038 clone 15, CB5038 clone 14, CB5038 clone 13
  • 218696
    • Treatment: DMSO (0.1%)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, CB5038 clone 17, CB5038 clone 16, CB5038 clone 15, CB5038 clone 14, CB5038 clone 13

Batch 10 (2020_09_09_Batch10)

Click to expand plate contents [8 plates]

• 8 plates
  • 218852
    • Treatment: DMSO (0.1%)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, CB5038 clone 17, CB5038 clone 16, CB5038 clone 15, CB5038 clone 14, CB5038 clone 13
  • 218853
    • Treatment: CB-5083 (700 nM)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, CB5038 clone 17, CB5038 clone 16, CB5038 clone 15, CB5038 clone 14, CB5038 clone 13
  • 218854
    • Treatment: DMSO (0.1%)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, Ixazomib clone 01, Ixazomib clone 02, Ixazomib clone 03, Ixazomib clone 04, Ixazomib clone 05
  • 218855
    • Treatment: Ixazomib (50 nM)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, Ixazomib clone 01, Ixazomib clone 02, Ixazomib clone 03, Ixazomib clone 04, Ixazomib clone 05
  • 218856
    • Treatment: DMSO (0.1%)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, CB5038 clone 17, CB5038 clone 16, CB5038 clone 15, CB5038 clone 14, CB5038 clone 13
  • 218857
    • Treatment: CB-5083 (700 nM)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, CB5038 clone 17, CB5038 clone 16, CB5038 clone 15, CB5038 clone 14, CB5038 clone 13
  • 218858
    • Treatment: DMSO (0.1%)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, Ixazomib clone 01, Ixazomib clone 02, Ixazomib clone 03, Ixazomib clone 04, Ixazomib clone 05
  • 218859
    • Treatment: Ixazomib (50 nM)
    • Clones: WT Parental, WT Clone 07, WT Clone 06, WT Clone 05, WT Clone 04, Ixazomib clone 01, Ixazomib clone 02, Ixazomib clone 03, Ixazomib clone 04, Ixazomib clone 05

Audit

Below, I report Percent Strong for each plate. For a full report see the figures in https://github.com/broadinstitute/profiling-resistance-mechanisms/tree/7e5ee27021816012297c38d58088438eb7ad3a53/1.profiling-audit/figures

Plate	Batch	Perturbation	Percent Strong
218775	2020_08_24_Batch9	CB-5083 (700 nM)	65.33%
218774	2020_08_24_Batch9	DMSO (0.1%)	55.33%
218699	2020_08_24_Batch9	Ixazomib (50 nM)	87.33%
218698	2020_08_24_Batch9	DMSO (0.1%)	87.33%
218697	2020_08_24_Batch9	CB-5083 (700 nM)	75.33%
218696	2020_08_24_Batch9	DMSO (0.1%)	74.67%
218852	2020_09_09_Batch10	DMSO (0.1%)	60%
218853	2020_09_09_Batch10	CB-5083 (700 nM)	59.33%
218854	2020_09_09_Batch10	DMSO (0.1%)	52%
218855	2020_09_09_Batch10	Ixazomib (50 nM)	67.33%
218856	2020_09_09_Batch10	DMSO (0.1%)	40%
218857	2020_09_09_Batch10	CB-5083 (700 nM)	57.33%
218858	2020_09_09_Batch10	DMSO (0.1%)	71.33%
218859	2020_09_09_Batch10	Ixazomib (50 nM)	58.67%

Limitation

All plates in both batches include the same treatment in all wells. This prevents us from normalizing per plate. We will need to normalize all plates together and then adjust for batch effects.