|
| Status |
Public on Apr 10, 2018 |
| Title |
Sleep deprived subject 6341 blood collection 03 [D8] |
| Sample type |
RNA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: s6341
fatigue_category: susceptible
subject group: Sleep Deprived
study phase: baseline
timepoint: t03
|
| Treatment protocol |
Blood was drawn every 4 hours during time awake on day 2 (Baseline), day 4 (Experimental), and day 6 (Recovery) of the 7 days in the sleep lab, amounting to 4 draws per day for 12 total timepoints per subject. On all 7 days, Control (C) subjects had 10 h TIB. The Sleep Deprived (SD) subjects experienced 10 h TIB during Baseline and Recovery days, but underwent 62 h continued wakefulness in the Experimental phase. Blood draws on day 4 (Experimental) for the Sleep Deprived subjects correspond to hours 24-36 of continued wakefulness.
|
| Growth protocol |
Blood was collected in PAXgene tubes from healthy adult human volunteers.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from blood collected in PAXgene™ tubes using a QIAcube robotic workstation (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Reverse transcription was performed with Ovation Pico WTA System V2 kit (NuGEN), and fragmentation and biotin labeling was performed using the Encore® Biotin module (NuGEN).
|
| |
|
| Hybridization protocol |
Hybridization cocktail was prepared according to the NuGEN Encore® Biotin module manual. Affymetrix GeneChip Human Gene 1.0 ST arrays were prewet with hybridization solution, and then incubated with hybridization cocktail.
|
| Scan protocol |
Affymetrix Wash and Stain kit reagents and fluidics protocol were used with the GeneChip Fluidics Station 450 for post-hybridization chip processing. Scanning was done on an Affymetrix Scanner with G7 upgrade.
|
| Description |
SD_6341_t03
Reanalysis of sample SD_6341_t03 in GSE98564
|
| Data processing |
Transcript Cluster-level expression data was derived with the RMA algorithm in the R/oligo package v. 1.32.0. Data were filtered for low expression, only retaining a Transcript Cluster if at least 6 samples had log2 expression >6. This Series contains values for all cel files in GSE98564 excepting 6 cel files identified as outliers.
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| |
|
| Submission date |
May 04, 2017 |
| Last update date |
Apr 10, 2018 |
| Contact name |
Hilary A Uyhelji |
| Organization name |
Federal Aviation Administration
|
| Department |
Civil Aerospace Medical Institute
|
| Street address |
6500 S. MacArthur Blvd.
|
| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73169 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE98565 |
Gene expression biomarkers for neurobehavioral impairment from total sleep deprivation microarray data [D8] |
| GSE98582 |
Exploring gene expression biomarker candidates for neurobehavioral impairment from total sleep deprivation |
|
