README.md

In jmw86069/farrisdata: Farris et al 2019, mouse hippocampus RNA-seq data objects

farrisdata

R package containing gene and transcript expression data supporting the Farris et al 2019 paper: Hippocampal Subregions Express Distinct Dendritic Transcriptomes that Reveal Differences in Mitochondrial Function in CA2. Cell Rep. 2019 Oct 8;29(2):522-539.e6. doi: 10.1016/j.celrep.2019.08.093.

The Splicejam Web App is online: http://splicejam.vtc.vt.edu/

This farrisdata data is intended for analysis using the jampack R package, which ultimately uses the splicejam package for data visualization.

See:

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

How to install

Install using the R package remotes and this command:

remotes::install_github("jmw86069/farrisdata")

Quick Usage

# install R packages if necessary
remotes::install_github("jmw86069/farrisdata")
remotes::install_github("jmw86069/splicejam")

# Run the Splicejam Web Shiny App
library(splicejam)
launchSashimiApp()

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.

Additional Citations:

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. 14, 2024, 6:29 p.m.