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K562 shRNA essentiality screen: count table

Source: R/k562_data.R
k562_count_table.Rd

Read counts of a published genome-wide shRNA essentiality screen in K562 cells (Morgens et al. 2016), with reference essential and non-essential genes (k562_reference_genes). In an essentiality screen the cells are grown for some time after the infection with the library: the barcodes of the genes needed for growth (essential genes) are depleted. Since the essential genes are known, the dataset can be used to evaluate how well a method finds the true hits.

Usage

data(k562_count_table)

Format

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

Barcode

The shRNA identifier. It starts with the NCBI (Entrez) gene ID of the targeted gene (0 for the non-targeting controls).

Plasmid

The counts in the plasmid library, before the screen.

T14_A, T14_B

The counts of the two replicates after 14 days of growth.

Source

Morgens DW, Deans RM, Li A, Bassik MC (2016). Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. Nat Biotechnol 34:634-636. doi:10.1038/nbt.3567

Details

To keep the package small, the dataset is a subset of the original library (about 500,000 shRNAs): all the shRNAs of the 681 core essential and 904 non-essential reference genes, of 1000 other randomly chosen genes and 1000 randomly chosen non-targeting controls. The script that builds the subset is in the scripts folder of the installed package (system.file("scripts", package = "ScreenR")); the licenses of the original data are in system.file("LICENSES_data.txt", package = "ScreenR").

The counts come from the test data of the casTLE software (https://bitbucket.org/dmorgens/castle), distributed under the BSD-2-Clause license, Copyright (c) 2016, David W Morgens.

See also

k562_annotation_table, k562_reference_genes

Examples

data(k562_count_table)
data(k562_annotation_table)
head(k562_count_table)
#>        Barcode Plasmid T14_A T14_B
#> 1 0_H01__01204      68    19    55
#> 2 0_H01__01217      69    53    75
#> 3 0_H01__01229      49     2     7
#> 4 0_H01__01247      62    77   124
#> 5 0_H01__01258      56   165   196
#> 6 0_H01__01278     141   105   180

# The sample names do not follow the Day_Treatment_Replicate convention,
# so the samples are described with a sample table: the plasmid and day 14
# are the time points, and the screen has no treatment
samples <- data.frame(
    Sample = c("Plasmid", "T14_A", "T14_B"),
    Day = c("Plasmid", "T14", "T14"),
    Treatment = "Untreated"
)
object <- create_screenr_object(
    table = k562_count_table, annotation = k562_annotation_table,
    groups = factor(c("Plasmid", "T14", "T14")),
    sample_table = samples
)