Read counts per gene for airway smooth muscle cell lines RNA-Seq experiment
data("airway")data("airway_treat")
data("airway_four_columns")
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:
Number of reads for the specific gene in all treated samples.
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:
Number of reads for the specific gene in all treated samples.
Number of reads for the specific gene in all untreated samples.
Number of reads for all other genes in all treated samples.
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 | \(X_{i, 2}\) | \(X_{i, 4}\) |
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.
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). tools:::Rd_expr_doi("https://doi.org/10.1371/journal.pone.0099625")