K562 shRNA essentiality screen: annotation table — k562_annotation_table • ScreenR

Annotation of the shRNAs of k562_count_table.

Usage

data(k562_annotation_table)

Format

A data frame with 67358 rows (shRNAs) and 4 columns:

Barcode: The shRNA identifier, as in k562_count_table.
Gene: The symbol of the targeted gene ("non-targeting" for the controls).
Gene_ID: The NCBI (Entrez) gene ID (NA for the controls).
Class: "core essential" or "non-essential" for the reference genes (see k562_reference_genes), "other" for the other genes and "non-targeting" for the controls.

Source

Morgens DW et al. (2016) Nat Biotechnol 34:634-636. doi:10.1038/nbt.3567 . Gene symbols from the NCBI gene_info file distributed with casTLE.

See also

k562_count_table

Examples

data(k562_annotation_table)
table(k562_annotation_table$Class)
#> 
#> core essential  non-essential  non-targeting          other 
#>          17648          22775           1000          25935