airway {DiscreteDatasets}

Airway smooth muscle cells

Description

Read counts per gene for airway smooth muscle cell lines RNA-Seq experiment

Usage

data("airway")

data("airway_treat")

data("airway_four_columns")

Format

airway is a data.frame with 63,677 rows and 8 columns. Each row corresponds to a specific gene and each column to a labeled sample.

airway_treat is a data.frame with 63,677 rows representing genes with the following two columns:

Treatment

Number of reads for the specific gene in all treated samples.

NoTreatment

Number of reads for the specific gene in all untreated samples.

Thus, each line describes a 2x2 table, e.g.:

ENSG00000000003	This gene	All other genes
Treatment	X_{i, 1}	89,561,179 - X_{i, 1}
No Treatment	X_{i, 2}	85,955,244 - X_{i, 2}

airway_four_columns is a data.frame with 63,677 rows representing genes with the following four columns:

Treatment.ThisGene

Number of reads for the specific gene in all treated samples.

NoTreatment.ThisGene

Number of reads for the specific gene in all untreated samples.

Treatment.AllOtherGenes

Number of reads for all other genes in all treated samples.

NoTreatment.AllOtherGenes

Number of reads for tall other genes in all untreated samples.

Thus, each line describes a 2x2 table, e.g.:

ENSG00000000003	This gene	All other genes
Treatment	X_{i, 1}	X_{i, 3}
No Treatment	X_{i, 2}	X_{i, 4}

Details

The cell lines of the even-numbered samples were treated with dexamethasone, whereas the cell lines of the odd-numbered samples were not. There were 89,561,179 reads for all treated samples and 85,955,244 for the untreated ones.

Note

The original airway dataset has been taken from the airway BioConductor package. Since the original data would require other BioConductor packages to access it, it has been reformatted to a standard data frame (with assay(airway)) which only contains the raw numeric data.

Source

FASTQ files from SRA, phenotypic data from GEO

References

Himes, B. E., Jiang, X., Wagner, P., Hu, R., Wang, Q., Klanderman, B., Whitaker, R. M., Duan, Q., Lasky-Su, J., Nikolos, C., Jester, W., Johnson, M., Panettieri, R. Jr., Tantisira, K. G., Weiss, S. T., Lu, Q. (2014). RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells. PLoS One 9(6). doi:10.1371/journal.pone.0099625