GBC - gRNA dictionary?

[Tian Luyi]

Hi Atray,

Do you know where can I find the GBC-gRNA dictionary? https://github.com/asncd/MIMOSCA/blob/master/GBC_CBC_pairing/small_data/dc_pool.csv seems to be a small sample but I wonder if I can have a complete list.

Luyi

[Atray Dixit]

Hi Luyi,

You can find them under their respective sample id's in GEO here

They'll be named something like samplename_cbc_gbc_dict_.csv.gz

Best,

Atray

[Tian Luyi]

but they are cell barcode - gRNA association. I just wonder if there are gRNA - gRNA barcode association. If I understand the method correctly one gRNA should not have only one associated barcode(GBC not CBC), is that correct? 

[Atray Dixit]

Hi Tian,

My apologies. It depends on the manner in which cloning is performed. If, as in most of our experiments, cloning is performed for each sgRNA separately, then each sgRNA will be uniquely associated with a GBC. If, as we did in our supplementary experiment ( FigS5) it is done in one pool with a high diversity GBC plasmid vector, then there will be multiple GBCs per sgRNA.

I've uploaded the additional mappings for the cell cycle and K562 transcription factor screens here and in the same location that the dc_pool.csv file was found in the github.

Let me know if you have any more questions.

Atray