Acosta-Alvear D, Zhou Y, Blais A, Tsikitis M, Lents NH, Arias C, Lennon CJ, Kluger Y, Dynlacht BD. XBP1 controls diverse cell type- and condition-specific transcriptional regulatory networks. Mol Cell. 2007;27(1):53–66.
Article
CAS
PubMed
Google Scholar
Anafi RC, Pellegrino R, Shockley KR, Romer M, Tufik S, Pack AI. Sleep is not just for the brain: transcriptional responses to sleep in peripheral tissues. BMC Genomics. 2013;14:362.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bekker-Jensen S, Rendtlew Danielsen J, Fugger K, Gromova I, Nerstedt A, Lukas C, Bartek J, Lukas J, Mailand N. HERC2 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Nat Cell Biol. 2010;12(1):80–6 sup pp 81–12.
Article
CAS
PubMed
Google Scholar
Bellesi M, Bushey D, Chini M, Tononi G, Cirelli C. Contribution of sleep to the repair of neuronal DNA double-strand breaks: evidence from flies and mice. Sci Rep. 2016;6:36804.
Article
CAS
PubMed
PubMed Central
Google Scholar
Benjamini Y, Hochberg Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J Royal Stat Soc Series B-Methodol. 1995;57(1):289–300.
Google Scholar
Bonanno L, Costa C, Majem M, Sanchez JJ, Rodriguez I, Gimenez-Capitan A, Molina-Vila MA, Vergnenegre A, Massuti B, Favaretto A, Rugge M, Pallares C, Taron M, Rosell R. Combinatory effect of BRCA1 and HERC2 expression on outcome in advanced non-small-cell lung cancer. BMC Cancer. 2016;16:312.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cai Y, Dai Y, Wang Y, Yang Q, Guo J, Wei C, Chen W, Huang H, Zhu J, Zhang C, Zheng W, Wen Z, Liu H, Zhang M, Xing S, Jin Q, Feng CG, Chen X. Single-cell transcriptomics of blood reveals a natural killer cell subset depletion in tuberculosis. EBioMedicine. 2020;53:102686.
Article
PubMed
PubMed Central
Google Scholar
Chen R, Wu X, Jiang L, Zhang Y. Single-cell RNA-Seq reveals hypothalamic cell diversity. Cell Rep. 2017;18(13):3227–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chung S, Weber F, Zhong P, Tan CL, Nguyen TN, Beier KT, Hormann N, Chang WC, Zhang Z, Do JP, Yao S, Krashes MJ, Tasic B, Cetin A, Zeng H, Knight ZA, Luo L, Dan Y. Identification of preoptic sleep neurons using retrograde labelling and gene profiling. Nature. 2017;545(7655):477–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cirelli C, Gutierrez CM, Tononi G. Extensive and divergent effects of sleep and wakefulness on brain gene expression. Neuron. 2004;41(1):35–43.
Article
CAS
PubMed
Google Scholar
Cohen J. Statistical power analysis for the behavioral sciences. New York: Routledge Academic; 1988.
Google Scholar
Curie T, Mongrain V, Dorsaz S, Mang GM, Emmenegger Y, Franken P. Homeostatic and circadian contribution to EEG and molecular state variables of sleep regulation. Sleep. 2013;36(3):311–23.
Article
PubMed
PubMed Central
Google Scholar
Eisele S, Krumbholz M, Fischer MT, Mohan H, Junker A, Arzberger T, Hohlfeld R, Bradl M, Lassmann H, Meinl E. Prospects of transcript profiling for mRNAs and MicroRNAs using formalin-fixed and paraffin-embedded dissected autoptic multiple sclerosis lesions. Brain Pathol. 2012;22(5):607–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Franken P, Dijk DJ, Tobler I, Borbely AA. Sleep-deprivation in rats - effects on Eeg power spectra, vigilance states, and cortical temperature. Am J Physiol. 1991;261(1):R198–208.
CAS
PubMed
Google Scholar
Franklin K, Paxinos G. The Mouse Brain in Stereotaxic Coordinates, Elsevier (3rd Edition); 2008.
Google Scholar
Gaus SE, Strecker RE, Tate BA, Parker RA, Saper CB. Ventrolateral preoptic nucleus contains sleep-active, galaninergic neurons in multiple mammalian species. Neuroscience. 2002;115(1):285–94.
Article
CAS
PubMed
Google Scholar
Gong H, McGinty D, Guzman-Marin R, Chew KT, Stewart D, Szymusiak R. Activation of c-fos in GABAergic neurones in the preoptic area during sleep and in response to sleep deprivation. J Physiol. 2004;556(Pt 3):935–46.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gong H, Szymusiak R, King J, Steininger T, McGinty D. Sleep-related c-Fos protein expression in the preoptic hypothalamus: effects of ambient warming. Am J Physiol Regul Integr Comp Physiol. 2000;279(6):R2079–88.
Article
CAS
PubMed
Google Scholar
Groelz D, Sobin L, Branton P, Compton C, Wyrich R, Rainen L. Non-formalin fixative versus formalin-fixed tissue: a comparison of histology and RNA quality. Exp Mol Pathol. 2013;94(1):188–94.
Article
CAS
PubMed
Google Scholar
Guo X, Keenan BT, Sarantopoulou D, Lim DC, Lian J, Grant GR, Pack AI. Age attenuates the transcriptional changes that occur with sleep in the medial prefrontal cortex. Aging Cell. 2019;18(6):e13021.
CAS
PubMed
PubMed Central
Google Scholar
Hoekstra MM, Emmenegger Y, Hubbard J, Franken P. Cold-inducible RNA-binding protein (CIRBP) adjusts clock-gene expression and REM-sleep recovery following sleep deprivation. Elife. 2019;8:e43400.
Article
PubMed
PubMed Central
Google Scholar
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
Article
CAS
Google Scholar
John J, Kumar VM. Effect of NMDA lesion of the medial preoptic neurons on sleep and other functions. Sleep. 1998;21(6):587–98.
Article
CAS
PubMed
Google Scholar
Jones W, Greytak S, Odeh H, Guan P, Powers J, Bavarva J, Moore HM. Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles. Sci Rep. 2019;9(1):6980.
Article
PubMed
PubMed Central
CAS
Google Scholar
Khodosevich K, Inta D, Seeburg PH, Monyer H. Gene expression analysis of in vivo fluorescent cells. PLoS One. 2007;2(11):e1151.
Article
PubMed
PubMed Central
CAS
Google Scholar
Korhonen MK, Vuorenmaa E, Nystrom M. The first functional study of MLH3 mutations found in cancer patients. Genes Chromosomes & Cancer. 2008;47(9):803–9.
Article
CAS
Google Scholar
Koyama Y, Hayaishi O. Firing of neurons in the preoptic/anterior hypothalamic areas in rat: its possible involvement in slow wave sleep and paradoxical sleep. Neurosci Res. 1994;19(1):31–8.
Article
CAS
PubMed
Google Scholar
Kroeger D, Absi G, Gagliardi C, Bandaru SS, Madara JC, Ferrari LL, Arrigoni E, Munzberg H, Scammell TE, Saper CB, Vetrivelan R. Galanin neurons in the ventrolateral preoptic area promote sleep and heat loss in mice. Nat Commun. 2018;9(1):4129.
Article
PubMed
PubMed Central
CAS
Google Scholar
Landry M, Roche D, Angelova E, Calas A. Expression of galanin in hypothalamic magnocellular neurones of lactating rats: co-existence with vasopressin and oxytocin. J Endocrinol. 1997;155(3):467–81.
Article
CAS
PubMed
Google Scholar
Law CW, Alhamdoosh M, Su S, Dong X, Tian L, Smyth GK, Ritchie ME. RNA-seq analysis is easy as 1–2-3 with limma, Glimma and edgeR. F1000Res. 2016;5:1408.
Article
CAS
Google Scholar
Letzkus M, Luesink E, Starck-Schwertz S, Bigaud M, Mirza F, Hartmann N, Gerstmayer B, Janssen U, Scherer A, Schumacher MM, Verles A, Vitaliti A, Nirmala N, Johnson KJ, Staedtler F. Gene expression profiling of immunomagnetically separated cells directly from stabilized whole blood for multicenter clinical trials. Clin Transl Med. 2014;3:36.
Article
PubMed
PubMed Central
Google Scholar
Liberzon A. A description of the molecular signatures database (MSigDB) web site. Methods Mol Biol. 2014;1150:153–60.
Article
CAS
PubMed
Google Scholar
Lipkin SM, Wang V, Jacoby R, Banerjee-Basu S, Baxevanis AD, Lynch HT, Elliott RM, Collins FS. MLH3: a DNA mismatch repair gene associated with mammalian microsatellite instability. Nat Genet. 2000;24(1):27–35.
Article
CAS
PubMed
Google Scholar
Mackiewicz M, Shockley KR, Romer MA, Galante RJ, Zimmerman JE, Naidoo N, Baldwin DA, Jensen ST, Churchill GA, Pack AI. Macromolecule biosynthesis: a key function of sleep. Physiol Genomics. 2007;31(3):441–57.
Article
CAS
PubMed
Google Scholar
Madabhushi R, Gao F, Pfenning AR, Pan L, Yamakawa S, Seo J, Rueda R, Phan TX, Yamakawa H, Pao PC, Stott RT, Gjoneska E, Nott A, Cho S, Kellis M, Tsai LH. Activity-induced DNA breaks govern the expression of neuronal early-response genes. Cell. 2015;161(7):1592–605.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maret S, Dorsaz S, Gurcel L, Pradervand S, Petit B, Pfister C, Hagenbuchle O, O'Hara BF, Franken P, Tafti M. Homer1a is a core brain molecular correlate of sleep loss. Proc Natl Acad Sci U S A. 2007;104(50):20090–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
McGinty DJ, Sterman MB. Sleep suppression after basal forebrain lesions in the cat. Science. 1968;160(3833):1253–5.
Article
CAS
PubMed
Google Scholar
Moffitt JR, Bambah-Mukku D, Eichhorn SW, Vaughn E, Shekhar K, Perez JD, Rubinstein ND, Hao J, Regev A, Dulac C, Zhuang X. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science. 2018;362(6416):eaau5324.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mongrain V, Hernandez SA, Pradervand S, Dorsaz S, Curie T, Hagiwara G, Gip P, Heller HC, Franken P. Separating the contribution of glucocorticoids and wakefulness to the molecular and electrophysiological correlates of sleep homeostasis. Sleep. 2010;33(9):1147–57.
Article
PubMed
PubMed Central
Google Scholar
Morf J, Rey G, Schneider K, Stratmann M, Fujita J, Naef F, Schibler U. Cold-inducible RNA-binding protein modulates circadian gene expression posttranscriptionally. Science. 2012;338(6105):379–83.
Article
CAS
PubMed
Google Scholar
Naidoo N, Davis JG, Zhu J, Yabumoto M, Singletary K, Brown M, Galante R, Agarwal B, Baur JA. Aging and sleep deprivation induce the unfolded protein response in the pancreas: implications for metabolism. Aging Cell. 2014;13(1):131–41.
Article
CAS
PubMed
Google Scholar
Nikonova EV, Gilliland JD, Tanis KQ, Podtelezhnikov AA, Rigby AM, Galante RJ, Finney EM, Stone DJ, Renger JJ, Pack AI, Winrow CJ. Transcriptional Profiling of Cholinergic Neurons From Basal Forebrain Identifies Changes in Expression of Genes Between Sleep and Wake. Sleep. 2017;40(6):zsx059.
Article
PubMed Central
Google Scholar
Pinto RM, Dragileva E, Kirby A, Lloret A, Lopez E, Claire JS, Panigrahi GB, Hou C, Holloway K, Gillis T, Guide JR, Cohen PE, Li GM, Pearson CE, Daly MJ, Wheeler VC. Mismatch repair genes Mlh1 and Mlh3 modify CAG instability in Huntington's disease mice: genome-wide and candidate approaches. PLoS Genet. 2013;9(10):e1003930.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ritchie ME, Phipson B, Wu D, Hu YF, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research. 2015;43(7):e47.
Article
PubMed
PubMed Central
CAS
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.
Article
CAS
PubMed
Google Scholar
Saper CB, Chou TC, Scammell TE. The sleep switch: hypothalamic control of sleep and wakefulness. Trends Neurosci. 2001;24(12):726–31.
Article
CAS
PubMed
Google Scholar
Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3(6):1101–8.
Article
CAS
PubMed
Google Scholar
Shen XH, Ellis RE, Sakaki K, Kaufman RJ. Genetic interactions due to constitutive and inducible gene regulation mediated by the unfolded protein response in C-elegans. PLoS Genet. 2005;1(3):355–68.
Article
CAS
Google Scholar
Sherin JE, Elmquist JK, Torrealba F, Saper CB. Innervation of histaminergic tuberomammillary neurons by GABAergic and galaninergic neurons in the ventrolateral preoptic nucleus of the rat. J Neurosci. 1998;18(12):4705–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sherin JE, Shiromani PJ, McCarley RW, Saper CB. Activation of ventrolateral preoptic neurons during sleep. Science. 1996;271(5246):216–9.
Article
CAS
PubMed
Google Scholar
Steininger TL, Gong H, McGinty D, Szymusiak R. Subregional organization of preoptic area/anterior hypothalamic projections to arousal-related monoaminergic cell groups. J Comp Neurol. 2001;429(4):638–53.
Article
CAS
PubMed
Google Scholar
Suntsova N, Szymusiak R, Alam MN, Guzman-Marin R, McGinty D. Sleep-waking discharge patterns of median preoptic nucleus neurons in rats. J Physiol. 2002;543(Pt 2):665–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Szymusiak R, Alam N, Steininger TL, McGinty D. Sleep-waking discharge patterns of ventrolateral preoptic/anterior hypothalamic neurons in rats. Brain Res. 1998;803(1–2):178–88.
Article
CAS
PubMed
Google Scholar
Szymusiak R, Satinoff E. Ambient temperature-dependence of sleep disturbances produced by basal forebrain damage in rats. Brain Res Bull. 1984;12(3):295–305.
Article
CAS
PubMed
Google Scholar
Taylor RC, Dillin A. XBP-1 is a cell-nonautonomous regulator of stress resistance and longevity. Cell. 2013;153(7):1435–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thompson CL, Wisor JP, Lee CK, Pathak SD, Gerashchenko D, Smith KA, Fischer SR, Kuan CL, Sunkin SM, Ng LL, Lau C, Hawrylycz M, Jones AR, Kilduff TS, Lein ES. Molecular and anatomical signatures of sleep deprivation in the mouse brain. Front Neurosci. 2010;4:165.
Article
PubMed
PubMed Central
CAS
Google Scholar
Vecsey CG, Peixoto L, Choi JHK, Wimmer M, Jaganath D, Hernandez PJ, Blackwell J, Meda K, Park AJ, Hannenhalli S, Abel T. Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus. Physiol Genomics. 2012;44(20):981–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
von Ahlfen S, Missel A, Bendrat K, Schlumpberger M. Determinants of RNA quality from FFPE samples. PLoS One. 2007;2(12):e1261.
Article
CAS
Google Scholar
Wu D, Smyth GK. Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Res. 2012;40(17):e133.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu Z, Cortes R, Villar M, Morino P, Castel MN, Hokfelt T. Evidence for upregulation of galanin synthesis in rat glial cells in vivo after colchicine treatment. Neurosci Lett. 1992;145(2):185–8.
Article
CAS
PubMed
Google Scholar
Zada D, Bronshtein I, Lerer-Goldshtein T, Garini Y, Appelbaum L. Sleep increases chromosome dynamics to enable reduction of accumulating DNA damage in single neurons. Nat Commun. 2019;10(1):895.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao S, Li CI, Guo Y, Sheng Q, Shyr Y. RnaSeqSampleSize: real data based sample size estimation for RNA sequencing. BMC Bioinformatics. 2018;19(1):191.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zheng Q, Huang T, Zhang L, Zhou Y, Luo H, Xu H, Wang X. Dysregulation of ubiquitin-proteasome system in neurodegenerative diseases. Front Aging Neurosci. 2016;8:303.
Article
PubMed
PubMed Central
CAS
Google Scholar