The aim of this experiment was to develop new methods to extract pure fractions of nuclear and cytoplasmic RNA. We compared the results of nuclear and cytoplasmic RNA-sequencing to results of the total and polyA+ RNA-sequencing. Cytoplasmic, nuclear, total and polyA+ RNA was extracted from two human brain samples and sequenced on the SOLiD system. We analyzed the data to look for differences in levels of nascent transcription and mature mRNAs between the different samples.