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.

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 version 0.12.0 was run using Gencode mouse reference transcripts M20, 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/extdata/coldata.csv file was obtained from the SraRunTable.txt downloaded directly from SRA. This file contains the phenotypic information about the 12 samples:

dir <- system.file("extdata", package="oct4")
coldata <- read.csv(file.path(dir,"coldata.csv"))
coldata

##         names line condition
## 1  SRX2236945 OCT4     untrt
## 2  SRX2236946 OCT4     untrt
## 3  SRX2236947 OCT4     untrt
## 4  SRX2236948 OCT4       trt
## 5  SRX2236949 OCT4       trt
## 6  SRX2236950 OCT4       trt
## 7  SRX2236951 BRG1     untrt
## 8  SRX2236952 BRG1     untrt
## 9  SRX2236953 BRG1     untrt
## 10 SRX2236954 BRG1       trt
## 11 SRX2236955 BRG1       trt
## 12 SRX2236956 BRG1       trt

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

sessionInfo()

## R version 4.0.0 (2020-04-24)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.11-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.11-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        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_4.0.0 magrittr_1.5   tools_4.0.0    stringi_1.4.6  knitr_1.28    
## [6] stringr_1.4.0  xfun_0.13      evaluate_0.14