# Experiment and sample description This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018 [doi: 10.1038/s41588-018-0046-7](https://doi.org/10.1038/s41588-018-0046-7). 6 donors were selected from those that had publicly available reads in ENA. The selection procress is recorded in the file `inst/scripts/ena_download.R`, the donors were chosen as all female, the sample having been received as frozen, and then the top 6 were chosen based on mean purity as recorded by the study authors. # Salmon quantification [Salmon](https://combine-lab.github.io/salmon/) version 0.12.0 was run using [Gencode](https://www.gencodegenes.org/) human reference transcripts v29, 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/scripts/ena_downloads.R` R script also shows how the column data file `coldata.csv` was generated. This file contains the phenotypic information about the 24 samples: ```{r} dir <- system.file("extdata", package="macrophage") coldata <- read.csv(file.path(dir,"coldata.csv")) coldata <- coldata[,c(1,2,3,5)] coldata ``` # SummarizedExperiment The package also contains a summarized experiment object created using the script in `inst/scripts/gse_create.R`. This object can be loaded with `data("gse")`. # Acknowledgments Thanks to the study authors for posting their data publicly and clearly labelling their data. # Session info ```{r} sessionInfo() ```