Long noncoding RNAs (lncRNAs) have been detected in nearly every cell type and 
found to be fundamentally involved in many biological processes. The 
characterization of lncRNAs has immense potential to advance our comprehensive 
understanding of cellular processes and gene regulation, along with implications 
for the treatment of human disease. The recent ENCODE (Encyclopedia of DNA 
Elements) study reported 9,640 lncRNA loci in the human genome, which 
corresponds to around half the number of protein-coding genes. Because of this 
sheer number and their functional diversity, it is crucial to identify a pool of 
potentially relevant lncRNAs early on in a given study. In this review, we 
evaluate the methods for isolating lncRNAs by immunoprecipitation and review the 
advantages, disadvantages, and applications of three widely used approaches - 
microarray, tiling array, and RNA-seq - for identifying lncRNAs involved in gene 
regulation. We also look at ways in which data from publicly available databases 
such as ENCODE can support the study of lncRNAs.