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. Salmon was run
with 20 Gibbs inferential replicates per sample (see the Snakefile), but
these were removed as of version 1.9.1 to reduce the package size, and
num_bootstraps in each aux_info/meta_info.json
was set to 0 accordingly.
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 trtThanks to the study authors for posting their data publicly and clearly labelling their data, and for James Ashmore for pointing me to this dataset.
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## loaded via a namespace (and not attached):
## [1] digest_0.6.39 R6_2.6.1 fastmap_1.2.0 xfun_0.61
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