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K562 10x Genomics reference data for CRISPR power analysis

K562_10x.Rd

Pre-computed pilot data from K562 chronic myelogenous leukemia cells generated using 10x Chromium technology. This is a reference dataset from 10x Genomics. Contains baseline gene expression parameters and library size information for power analysis of CRISPR-based perturbation experiments.

Usage

K562_10x

Format

A list with 3 elements:

baseline_expression_stats

Data frame with gene expression data (16,395 genes × 3 columns):

  • response_id: Character vector of Ensembl gene IDs

  • relative_expression: Numeric vector of relative expression levels (TPM/1e6 scale)

  • expression_size: Numeric vector of dispersion parameters (theta)

library_parameters

List containing:

  • UMI_per_cell: Maximum UMI per cell parameter (61,081)

  • variation: Variation parameter for PCR bias (0.421)

mapping_efficiency

Numeric. Mapping efficiency value (0.801)

Source

Paper: 10X Genomics dataset: 10k K562 cells

Author and Year: 10x Genomics (example data for K562), 2018

Details

This dataset was generated from K562 chronic myelogenous leukemia cells using single-cell RNA sequencing with 10x Chromium technology.

Cells Used in Relative Expression Estimate: All cells in high-moi condition

See also

get_pilot_data_from_package for accessing this data programmatically

Examples

data(K562_10x)
str(K562_10x)
#> List of 3
#>  $ baseline_expression_stats:'data.frame':	16395 obs. of  3 variables:
#>   ..$ response_id        : chr [1:16395] "ENSG00000243485" "ENSG00000241860" "ENSG00000286448" "ENSG00000237491" ...
#>   ..$ relative_expression: num [1:16395] 1.12e-07 7.65e-07 1.41e-07 6.94e-06 1.48e-05 ...
#>   ..$ expression_size    : num [1:16395] 414.4428 0.6555 0.0515 7.965 8.8552 ...
#>  $ library_parameters       :List of 2
#>   ..$ UMI_per_cell: num 61082
#>   ..$ variation   : num 0.421
#>  $ mapping_efficiency       : num 0.801