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.

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 version 0.12.0 was run using Gencode human reference transcripts v29, with a snakemake 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:

dir <- system.file("extdata", package="macrophage")
coldata <- read.csv(file.path(dir,"coldata.csv"))
coldata <- coldata[,c(1,2,3,5)]
coldata
##             names sample_id line_id condition_name
## 1  SAMEA103885102    diku_A  diku_1          naive
## 2  SAMEA103885347    diku_B  diku_1           IFNg
## 3  SAMEA103885043    diku_C  diku_1         SL1344
## 4  SAMEA103885392    diku_D  diku_1    IFNg_SL1344
## 5  SAMEA103885182    eiwy_A  eiwy_1          naive
## 6  SAMEA103885136    eiwy_B  eiwy_1           IFNg
## 7  SAMEA103885413    eiwy_C  eiwy_1         SL1344
## 8  SAMEA103884967    eiwy_D  eiwy_1    IFNg_SL1344
## 9  SAMEA103885368    fikt_A  fikt_3          naive
## 10 SAMEA103885218    fikt_B  fikt_3           IFNg
## 11 SAMEA103885319    fikt_C  fikt_3         SL1344
## 12 SAMEA103885004    fikt_D  fikt_3    IFNg_SL1344
## 13 SAMEA103885284    ieki_A  ieki_2          naive
## 14 SAMEA103885059    ieki_B  ieki_2           IFNg
## 15 SAMEA103884898    ieki_C  ieki_2         SL1344
## 16 SAMEA103885157    ieki_D  ieki_2    IFNg_SL1344
## 17 SAMEA103885111    podx_A  podx_1          naive
## 18 SAMEA103884919    podx_B  podx_1           IFNg
## 19 SAMEA103885276    podx_C  podx_1         SL1344
## 20 SAMEA103885021    podx_D  podx_1    IFNg_SL1344
## 21 SAMEA103885262    qaqx_A  qaqx_1          naive
## 22 SAMEA103885228    qaqx_B  qaqx_1           IFNg
## 23 SAMEA103885308    qaqx_C  qaqx_1         SL1344
## 24 SAMEA103884949    qaqx_D  qaqx_1    IFNg_SL1344

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

sessionInfo()
## R Under development (unstable) (2022-10-25 r83175)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
## [1] compiler_4.3.0 magrittr_2.0.3 tools_4.3.0    stringi_1.7.8  knitr_1.40    
## [6] stringr_1.4.1  xfun_0.34      evaluate_0.17