The subcellular localization of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localization of newly discovered lncRNAs involves time-consuming and costly experimental methods. We have created "lncATLAS," a comprehensive resource of lncRNA localization in human cells based on RNA-sequencing data sets. Altogether, 6768 GENCODE-annotated lncRNAs are represented across various compartments of 15 cell lines. We introduce relative concentration index (RCI) as a useful measure of localization derived from ensemble RNA-seq measurements. LncATLAS is accessible through an intuitive and informative webserver, from which lncRNAs of interest are accessed using identifiers or names. Localization is presented across cell types and organelles, and may be compared to the distribution of all other genes. Publication-quality figures and raw data tables are automatically generated with each query, and the entire data set is also available to download. LncATLAS makes lncRNA subcellular localization data available to the widest possible number of researchers. It is available at lncatlas.crg.eu.

We also acknowledge the support of the Spanish Ministry of Economy and Competitiveness, “Centro de Excelencia Severo Ochoa 2013-2017,” SEV-2012-0208. R.J. was supported by Ramón y Cajal RYC-2011-08851. This research was partly supported by the NCCR “RNA & Disease” funded by the Swiss National Science Foundation.