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
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.
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
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.
sessionInfo()
## R version 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-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
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] compiler_4.4.0 tools_4.4.0 knitr_1.46 xfun_0.43 evaluate_0.23