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A549 Sakellaropoulos Chromium reference data for CRISPR power analysis

A549_Sakellaropoulos.Rd

Pre-computed pilot data from A549 lung adenocarcinoma cells generated using 10x Chromium technology. Contains baseline gene expression parameters and library size information for power analysis of CRISPR-based perturbation experiments.

Usage

A549_Sakellaropoulos

Format

A list with 3 elements:

baseline_expression_stats

Data frame with gene expression data (20,406 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: 1.19e9 - Total expected distinct UMIs at saturation

  • size: 1.64 - ZTNB shape parameter

  • mu: 0.244 - ZTNB mean parameter

  • reads_norm: 11,759 - Normalization constant (reads per cell)

  • n_cells: 24,744 - Number of cells in pilot data

  • UMI_per_cell_at_saturation: 48,179 - Maximum UMI per cell at infinite sequencing depth

mapping_efficiency

Numeric. Mapping efficiency value (0.794)

Source

Paper: MethNet: a robust approach to identify regulatory hubs and their distal targets from cancer methylomes

Author and Year: Sakellaropoulos et al., 2024

Journal: Nature Communications

Accession: GSE236304

PMID: 37577603

Details

This dataset was generated from A549 lung adenocarcinoma cells using single-cell RNA sequencing with 10x Chromium technology.

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

The data has been processed to extract key statistical parameters needed for power analysis calculations.

See also

get_pilot_data_from_package for accessing this data programmatically

Examples

data(A549_Sakellaropoulos)
str(A549_Sakellaropoulos)
#> List of 3
#>  $ baseline_expression_stats:'data.frame':	20406 obs. of  3 variables:
#>   ..$ response_id        : chr [1:20406] "ENSG00000241860" "ENSG00000237491" "ENSG00000228794" "ENSG00000225880" ...
#>   ..$ relative_expression: num [1:20406] 3.92e-07 5.60e-06 8.59e-06 2.62e-07 1.93e-06 ...
#>   ..$ expression_size    : num [1:20406] 0.601 2.767 173.024 0.326 431.582 ...
#>  $ library_parameters       :List of 7
#>   ..$ method_used               : chr "ZTNB"
#>   ..$ L                         : num 1.19e+09
#>   ..$ size                      : num 1.64
#>   ..$ mu                        : num 0.244
#>   ..$ reads_norm                : num 11759
#>   ..$ n_cells                   : num 24744
#>   ..$ UMI_per_cell_at_saturation: num 48179
#>  $ mapping_efficiency       : num 0.794