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Cell lines names with ".311" #66

Closed DianaZagirova closed 11 months ago

DianaZagirova commented 1 year ago

Hello,

I have downloaded the file LINCS_DCIC_2021_CRISPRPert_PredictedRNAseq_ChDir_Sigs.gctx from the section "Computed Signatures for CycleGAN Predicted RNA-Seq-Like Profiles of L1000 Samples (Level 5)" of the download page. According to this data, 19 cell lines have the name ending with ".311" (for e.g. "A549.311"). Initially, I had assumed that this cell line was identical to "A549". However, there is separate record for "A549" in the downloaded file as well.

Could you please clarify what the difference between cell lines with ".311" endings from the regular cell lines?

sxie04 commented 1 year ago

Hi @DianaZagirova,

The cell line names were taken from the original LINCS L1000 profiles. The CLUE.io CONNECTOPEDIA gives the following explanation:

Cells that have been transfected by a particular Cas9-containing vector, such as 311 or 101, are named with the vector name appended to their cell line name. For example, HA1E cells that are transfected with 311 vector are named HA1E.311.