Show simple item record

dc.contributor.authorGerstner, JR
dc.contributor.authorKoberstein, JN
dc.contributor.authorWatson, AJ
dc.contributor.authorZapero, N
dc.contributor.authorRisso, D
dc.contributor.authorSpeed, TP
dc.contributor.authorFrank, MG
dc.contributor.authorPeixoto, L
dc.date.accessioned2021-02-04T01:46:03Z
dc.date.available2021-02-04T01:46:03Z
dc.date.issued2016-04-22
dc.identifierpii: 10.1186/s12864-016-3065-8
dc.identifier.citationGerstner, J. R., Koberstein, J. N., Watson, A. J., Zapero, N., Risso, D., Speed, T. P., Frank, M. G. & Peixoto, L. (2016). Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex. BMC GENOMICS, 17 (Suppl 8), https://doi.org/10.1186/s12864-016-3065-8.
dc.identifier.issn1471-2164
dc.identifier.urihttp://hdl.handle.net/11343/259469
dc.description.abstractBACKGROUND: Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence indicates that sleep is necessary for normal brain function and that sleep need is a tightly regulated process. Surprisingly, molecular mechanisms that determine sleep need are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need. Several studies have characterized differential gene expression changes following sleep deprivation. Much less is known, however, about changes in gene expression during the compensatory response to sleep deprivation (i.e. recovery sleep). RESULTS: In this study we present a comprehensive analysis of the effects of sleep deprivation and subsequent recovery sleep on gene expression in the mouse cortex. We used a non-traditional analytical method for normalization of genome-wide gene expression data, Removal of Unwanted Variation (RUV). RUV improves detection of differential gene expression following sleep deprivation. We also show that RUV normalization is crucial to the discovery of differentially expressed genes associated with recovery sleep. Our analysis indicates that the majority of transcripts upregulated by sleep deprivation require 6 h of recovery sleep to return to baseline levels, while the majority of downregulated transcripts return to baseline levels within 1-3 h. We also find that transcripts that change rapidly during recovery (i.e. within 3 h) do so on average with a time constant that is similar to the time constant for the discharge of sleep need. CONCLUSIONS: We demonstrate that proper data normalization is essential to identify changes in gene expression that are specifically linked to sleep deprivation and recovery sleep. Our results provide the first evidence that recovery sleep is comprised of two waves of transcriptional regulation that occur at different times and affect functionally distinct classes of genes.
dc.languageEnglish
dc.publisherBIOMED CENTRAL LTD
dc.titleRemoval of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex
dc.typeJournal Article
dc.identifier.doi10.1186/s12864-016-3065-8
melbourne.affiliation.departmentSchool of Mathematics and Statistics
melbourne.affiliation.facultyScience
melbourne.source.titleBMC Genomics
melbourne.source.volume17
melbourne.source.issueSuppl 8
dc.rights.licenseCC BY
melbourne.elementsid1212044
melbourne.contributor.authorSpeed, Terence
dc.identifier.eissn1471-2164
melbourne.accessrightsOpen Access


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record