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dc.contributor.authorKronman, Hope
dc.contributor.authorRichter, Felix
dc.contributor.authorLabonté, Benoit
dc.contributor.authorChandra, Ramesh
dc.creatorKronman, H.
dc.date.accessioned2019-06-19T13:21:14Z
dc.date.available2019-06-19T13:21:14Z
dc.date.issued2019-05-24
dc.identifier.urihttps://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85066927652&origin=inward
dc.identifier.urihttp://hdl.handle.net/10713/9561
dc.descriptionAll data are available on NCBI’s GEO database, and can be found under the Accession Number GSE121199.en_US
dc.description.abstractSubcellular RNAseq promises to dissect transcriptional dynamics but is not well characterized. Furthermore, FACS may introduce bias but has not been benchmarked genome-wide. Finally, D1 and D2 dopamine receptor-expressing medium spiny neurons (MSNs) of the nucleus accumbens (NAc) are fundamental to neuropsychiatric traits but have only a short list of canonical surface markers. We address these gaps by systematically comparing nuclear-FACS, whole cell-FACS, and RiboTag affinity purification from D1- and D2-MSNs. Using differential expression, variance partitioning, and co-expression, we identify the following trade-offs for each method. RiboTag-seq best distinguishes D1- and D2-MSNs but has the lowest transcriptome coverage. Nuclear-FACS-seq generates the most differentially expressed genes and overlaps significantly with neuropsychiatric genetic risk loci, but un-annotated genes hamper interpretation. Whole cell-FACS is more similar to nuclear-FACS than RiboTag, but captures aspects of both. Using pan-method approaches, we discover that transcriptional regulation is predominant in D1-MSNs, while D2-MSNs tend towards cytosolic regulation. We are also the first to find evidence for moderate sexual dimorphism in these cell types at baseline. As these results are from 49 mice (nmale = 39, nfemale = 10), they represent generalizable ground-truths. Together, these results guide RNAseq methods selection, define MSN transcriptomes, highlight neuronal sex differences, and provide a baseline for D1- and D2-MSNs. © 2019, The Author(s).en_US
dc.description.sponsorshipNational Institute on Drug Abuse (NIDA) P01DA008227; National Institute of Mental Health (NIMH) P50MH096890en_US
dc.description.urihttps://dx.doi.org/10.1038/s41598-019-44798-9en_US
dc.language.isoen_USen_US
dc.publisherNature Publishing Groupen_US
dc.relation.ispartofScientific Reportsen_US
dc.subjectmedium spiny neuronsen_US
dc.subjectfluorescence-activated cell sortingen_US
dc.subject.meshSequence Analysis, RNAen_US
dc.subject.meshCell Separationen_US
dc.subject.meshNucleus Accumbensen_US
dc.subject.meshVentral Striatumen_US
dc.titleBiology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neuronsen_US
dc.typeArticleen_US
dc.identifier.doi10.1038/s41598-019-44798-9
dc.relation.volume9


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