Data source in other cell lines

[ChenyuWang-Monica]

It seems that all data listed in the repo are from U2OS or A549 cell lines. Are there any data with compound perturbation on other cell lines?

[niranjchandrasekaran]

Hi @ChenyuWang-Monica, only U2OS or A549 were used for generating the JUMP dataset.

[cea33]

I noticed in the JUMP Cell painting dataset paper that A549 cell lines seemed to only be used in the pilot experiments. Is it possible to compare genetic perturbations in A549s against the database if it is in U2OSs? Would special normalization steps need to be taken in this case?

[niranjchandrasekaran]

Hi @cea33,

Is it possible to compare genetic perturbations in A549s against the database if it is in U2OSs?

That might be difficult. But for the most part, the genetic perturbation experiments in A549 in the pilot will most likely have a U2OS counterpart (unless I am misremembering the experiments). If you can let me know which specific pilot experiment that you are comparing against the large U2OS dataset, I may be able to advise better.

[cea33]

I am trying to compare against the broader JUMP database cpg0016. I have A549s which are ectopically expressing bacterial proteins and I would like to use cell paint to compare their morphology to the broader JUMP dataset to look for similarities.

[niranjchandrasekaran]

Hi @cea33, thank you for the additional details. We had some success matching U2OS to A549 in the cpg0000 dataset, but I suspect both batch effects and differences in the cell line would be dominant, making it difficult to match your dataset with cpg0016. Aligning using positive control compounds or sphering using negative controls help with data alignment, but I am unsure how effective they will be across cell lines. There is an upcoming manuscript from the lab that will provide more details about them. I will share them with you once the manuscript is online.

[niranjchandrasekaran]

Hi @cea33, the batch correction manuscript in now up on biorxiv: https://www.biorxiv.org/content/10.1101/2023.09.15.558001v1