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T_CD8 Shifrut reference data for CRISPR power analysis

T_CD8_Shifrut.Rd

Pre-computed pilot data from primary CD8+ T cells generated using 10x Chromium technology. Contains baseline gene expression parameters and library size information for power analysis of CRISPR-based perturbation experiments.

Usage

T_CD8_Shifrut

Format

A list with 3 elements:

baseline_expression_stats

Data frame with gene expression data (20,935 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 saturation curve parameters estimated using preseqR. Data-adaptively selected method: ZTNB. Contains:

  • method_used: "ZTNB" - Zero-truncated negative binomial method

  • L: 1.11e8 - Total expected distinct UMIs at saturation

  • size: 2.69 - ZTNB shape parameter

  • mu: 2.17 - ZTNB mean parameter

  • reads_norm: 19,435 - Normalization constant (reads per cell)

  • n_cells: 12,340 - Number of cells in pilot data

  • UMI_per_cell_at_saturation: 8,957 - Maximum UMI per cell at infinite sequencing depth

mapping_efficiency

Numeric. Mapping efficiency value (0.679)

Source

Paper: Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function

Author and Year: Shifrut et al., 2018

Journal: Cell

Accession: GSE119450

PMID: 30449619

Details

This dataset was generated from primary CD8+ T 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(T_CD8_Shifrut)
str(T_CD8_Shifrut)
#> List of 3
#>  $ baseline_expression_stats:'data.frame':	20935 obs. of  3 variables:
#>   ..$ response_id        : chr [1:20935] "ENSG00000238009" "ENSG00000241860" "ENSG00000237491" "ENSG00000228794" ...
#>   ..$ relative_expression: num [1:20935] 2.27e-07 4.66e-07 1.98e-05 1.25e-05 1.26e-06 ...
#>   ..$ expression_size    : num [1:20935] 355.245 408.681 0.811 8.116 2.517 ...
#>  $ library_parameters       :List of 7
#>   ..$ method_used               : chr "ZTNB"
#>   ..$ L                         : num 1.11e+08
#>   ..$ size                      : num 2.69
#>   ..$ mu                        : num 2.17
#>   ..$ reads_norm                : num 19435
#>   ..$ n_cells                   : num 12340
#>   ..$ UMI_per_cell_at_saturation: num 8957
#>  $ mapping_efficiency       : num 0.679