README.md

In jmw86069/farrisdata: Farris et al Mouse Hippocampus RNA-seq data objects

farrisdata

R package containing gene and transcript expression data supporting Farris et al Mouse hippocampal transcriptome RNA-seq analysis.

This data is intended for analysis using the jampack R package, also available through GitHub, see:

• https://github.com/jmw86069/jampack

This package includes a data.frame for use by splicejam::prepareSashimi() to create Sashimi coverage plots of transcriptome RNA-seq data, see:

• https://github.com/jmw86069/splicejam

How to install

Install using the R package devtools and this command:

devtools::install_github("jmw86069/farrisdata")

Contents

A full set of documentation is provided using the pkgdown::build_site() function, and is available here:

Full data reference

This package contains two reference SummarizedExperiment objects, which are described in more detail in the corresponding R help pages.

• farrisGeneSE gene-level Salmon pseudocounts.
• farrisTxSE transcript-level Salmon pseudocounts, and TPM values.

The package also provides three reference gene lists containing detected genes in hippocampal CA1 in mouse and rat (Nakayama et al. 2017, Ainsley et al., 2014, Cajigas et al. 2012).

Lastly, the package provides a color substitution vector colorSub, and several vectors with derived transcript features.

Literature references:

Nakayama, K., Ohashi, R., Shinoda, Y., Yamazaki, M., Abe, M., Fujikawa, A., Shigenobu, S., Futatsugi, A., Noda, M., Mikoshiba, K., Furuichi, T., Sakimura, K., Shiina, N., 2017. RNG105/caprin1, an RNA granule protein for dendritic mRNA localization, is essential for long-term memory formation. eLife 6, e29677. doi:10.7554/eLife.29677

Ainsley, J.A., Drane, L., Jacobs, J., Kittelberger, K.A., Reijmers, L.G., 2014. Functionally diverse dendritic mRNAs rapidly associate with ribosomes following a novel experience. Nature Communications 5, 4510. doi:10.1038/ncomms5510

Cajigas, I.J., Tushev, G., Will, T.J., tom Dieck, S., Fuerst, N., Schuman, E.M., 2012. The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imag-ing. Neuron 74, 453–466. doi:10.1016/j.neuron.2012.02.036

jmw86069/farrisdata documentation built on Oct. 8, 2019, 9:56 p.m.