# Experiment and sample description This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, "The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells" published in eLIFE, March 2017 [doi: 10.7554/eLife.22631](https://doi.org/10.7554/eLife.22631). All 12 samples from the experiment were re-quantified, which consists of three replicates each of OCT4 conditional cells treated with 1 micrograms/mL doxycycline for 24 hr and controls (see paper Materials and Methods), and Brg1 conditional cells treated with 4-hydroxytamoxifen for 72 hr and controls (see paper Materials and Methods). # Salmon quantification [Salmon](https://combine-lab.github.io/salmon/) version 0.12.0 was run using [Gencode](https://www.gencodegenes.org/) mouse reference transcripts M20, with a [snakemake](https://snakemake.readthedocs.io/en/stable/) script that can be seen in `inst/scripts/Snakemake` and with log output in `inst/scripts/snakemake.log`. The quantification output is in the `inst/extdata/quant` directory. The `quant.sf` files have been gzipped to preserve space, so they are stored as `quant.sf.gz`. There are 20 Gibbs inferential replicates for each sample. # Sample information The `inst/extdata/coldata.csv` file was obtained from the `SraRunTable.txt` downloaded directly from SRA. This file contains the phenotypic information about the 12 samples: ```{r} dir <- system.file("extdata", package="oct4") coldata <- read.csv(file.path(dir,"coldata.csv")) coldata ``` # Acknowledgments Thanks to the study authors for posting their data publicly and clearly labelling their data, and for James Ashmore for pointing me to this dataset. # Session info ```{r} sessionInfo() ```