Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment

Molly Estill, Efrain Ribeiro, Nancy J. Francoeur, Melissa L. Smith, Robert Sebra, Szu Ying Yeh, Ashley M. Cunningham, Eric J. Nestler, Li Shen

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


To better understand the full-length transcriptome of the nucleus accumbens (NAc)—a key brain reward region—in chronic cocaine treatment, we perform the first single molecule, long-read sequencing analysis using the Iso-seq method to detect 42,114 unique transcripts from mouse NAc polyadenylated RNA. Using GENCODE annotation as a reference, we find that over half of the Iso-seq derived transcripts are annotated, while 46% of them harbor novel splicing events in known genes; around 1% of them correspond to other types of novel transcripts, such as fusion, antisense and intergenic. Approximately 34% of the novel transcripts are matched with a compiled transcriptome assembled from published short-read data from various tissues, with the remaining 69% being unique to NAc. These data provide a more complete picture of the NAc transcriptome than existing annotations and can serve as a comprehensive reference for future transcriptomic analyses of this important brain reward region.

Original languageEnglish
Article number6729
JournalScientific Reports
Issue number1
StatePublished - Dec 2021


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