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Series GSE56931 Query DataSets for GSE56931
Status Public on Oct 02, 2014
Title Blood gene expression reveals reduced circadian rhythmicity in individuals resistant to sleep deprivation
Organism Homo sapiens
Experiment type Expression profiling by array
Summary To address whether changes in gene expression in blood cells with sleep loss are different in individuals resistant and sensitive to sleep deprivation (SD).
Blood draws every 4 hours during a 3-day study: 24-hour normal baseline, 38 hours of continuous wakefulness and subsequent recovery sleep, for a total of 19 time-points per subject, with every 2-hr psychomotor vigilance test (PVT) assessment when awake. Fourteen subjects who were previously identified as behaviourally resistant (n=7) or sensitive (n=7) to SD by PVT. Intervention consisted of 38 hours continuous wakefulness. We found 4,481 unique genes with a significant 24-hour diurnal rhythm during a normal sleep-wake cycle in blood (false discovery rate [FDR] <5%). Biological pathways were enriched for biosynthetic processes during sleep. After accounting for circadian effects, two genes (SREBF1 and CPT1A, both involved in lipid metabolism) exhibited small, but significant, linear changes in expression with the duration of SD (FDR<5%). The main change with SD was a reduction in the amplitude of the diurnal rhythm of expression of normally cycling probe sets. This reduction was noticeably higher in behaviourally resistant subjects than sensitive subjects, at any given p-value. Furthermore, blood cell type enrichment analysis showed that the expression pattern difference between sensitive and resistant subjects is mainly found in cells of myeloid origin, such as monocytes. Individual differences in behavioural effects of sleep deprivation are associated with differences in diurnal amplitude of gene expression for genes that show circadian rhythmicity.
Overall design Blood draws were done every 4 hours during a 3-day (+1 baseline day) study: 24-hour normal baseline (6 time points: day 1 8hr, 12hr, 16hr, 20hr, day 2 0hr, 4hr), 38 hours of continuous wakefulness (10 time points: day 2 8hr, 12hr, 16hr, 20hr, day 3 0hr, 4hr, 8hr, 12hr, 16hr, 20hr) and subsequent recovery sleep (3 time points: day 4 0hr, 4hr, 8hr), for a total of 19 time-points per subject, with every 2-hr psychomotor vigilance test (PVT) assessment when awake. The missing/failed samples were as following: Resistant subjects (total 10 samples): BH006 day 2 20hr, 12hr, BH003 day 2 12hr, 4hr, BH003 day 3 4hr, BH008 day 4 0hr, BH008 day 1 16hr, BH008 day 3 16hr 20hr, BH010 day 4 0hr; Sensitive subjects (total 7 samples): BH004 day 2 12hr and 1 more missing sample, BH026 day 2 4hr, BH007 day 2 20hr and 1 more missing sample, BH016 day 2 4hr, BH015 day 3 0hr.
Contributor(s) Shockley KR, Pack AI, Podtelezhinikov A
Citation(s) 25197809
Submission date Apr 21, 2014
Last update date Mar 04, 2015
Contact name Keith Shockley
Organization name NIEHS
Street address 111 TW Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
Platforms (1)
GPL10379 Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray [HuRSTA-2a520709]
Samples (249)
GSM1371587 patient BH015, high responder, male, day2, hour12, baseline
GSM1371588 patient BH005, high responder, female, day2, hour 4, baseline
GSM1371589 patient BH007, high responder, male, day2, hour12, baseline
BioProject PRJNA244978

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Supplementary file Size Download File type/resource
GSE56931_RAW.tar 1.2 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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