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Sample GSM2599922 Query DataSets for GSM2599922
Status Public on Apr 10, 2018
Title Sleep deprived subject 6307 blood collection 10 [D6]
Sample type RNA
 
Source name blood
Organism Homo sapiens
Characteristics subject id: s6307
fatigue_category: susceptible
subject group: Sleep Deprived
study phase: experimental
timepoint: t07
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_6307_t10
Sample SD_6307_t10 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.
 
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)
GSE98564 Gene expression biomarkers for neurobehavioral impairment from total sleep deprivation microarray data [D6]
GSE98582 Exploring gene expression biomarker candidates for neurobehavioral impairment from total sleep deprivation

Data table header descriptions
ID_REF
VALUE RMA log2 expression

Data table
ID_REF VALUE
7896742 7.867800418
7896746 9.001007309
7896748 6.21112163
7896750 5.772120053
7896752 9.644159267
7896817 6.904406846
7896878 5.825987408
7897006 5.787472092
7897068 6.803332036
7897078 8.330020935
7897119 6.108796816
7897172 7.672853403
7897236 6.040076483
7897288 5.544495298
7897305 5.779219645
7897370 7.876700251
7897404 8.019574422
7897482 7.100170514
7897522 8.067529771
7897527 7.038428325

Total number of rows: 8454

Table truncated, full table size 164 Kbytes.




Supplementary file Size Download File type/resource
GSM2599922_6307t10_061212_HuGene-1_0-st-v1_.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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