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broadinstitute / cell-health

Predicting Cell Health with Morphological Profiles
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What is "Chr2" in `Metadata_gene_name`? #2

Closed gwaybio closed 5 years ago

gwaybio commented 5 years ago

I assume that it means "Chromosome 2"? Is this correct? So there was a CRISPR guide to target anywhere on the gene? Or is this some kind of control?

I see that the number of CRISPR constructs targeting Chr2 is very high.

gene num constructs
Chr2 144
PSMA1 48
ORC4 48
POLR2D 48
PPIB 48
LacZ 24
Luc 24
... ...

cc @shntnu

shntnu commented 5 years ago

@gwaygenomics the answer is hidden away in the wiki, snipped below

Question:

Can you clarify what these mean?

CDK4_CYP27B1-2F Chr2 MAP4K1_ACTN4 Tsai_HEK293_4 Tsai_VEGFA-1 Wang_K562_22_Nongenic-1

Answer:

All of those annotations you asked about are non-genic cutting controls - sgRNAs that will cut the genome a set number of times in areas that are not within genes. As a result, we can say that effects of those guides are entirely due to dna damage caused by the editing process. Chr2 guides and the MAP4K1_ACTN4 genes cut once (Chr2 at a non-amplified non-genic region on chromosome 2, MAP4K1_ACTN4 in the space between those two genes on chromosome 19). The others cut multiple times.

gwaybio commented 5 years ago

Great! Thank you! I do remember reading this now that you post 👍