LIF interleukin 6 family cytokine
Dependent Cell Lines
CRISPR: 6/757 STRONGLY SELECTIVE
Gene Effect (CERES)
1. Melanoma (1.4e-07) n=46
2. Skin (5.9e-07) n=52
Gene Effect (DEMETER2)
Expression & CN
Copy Number log2(relative to ploidy + 1)
Expression: RNASeq files are aligned with STAR and quantified with RSEM, then TPM-normalized. Reported values are log2(TPM+1).
Copy number: The relative copy number pipeline used varies by cell line. For around 1000 lines, Sanger WES data was used, while for around 700 lines, Broad WES data was used. The remaining lines use SNP array data as explained in 10.1038/s41586-019-1186-3. See 10.1101/720243 for details on how CN source is chosen per line. Lines with WES data were processed through GATK using PONs from TCGA without matched normals and transformed by log2(x+1).
# of cell lines