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Sample GSM2599907 Query DataSets for GSM2599907
Status Public on Apr 10, 2018
Title Sleep deprived subject 6291 blood collection 04 [D6]
Sample type RNA
 
Source name blood
Organism Homo sapiens
Characteristics subject id: s6291
fatigue_category: susceptible
subject group: Sleep Deprived
study phase: baseline
timepoint: t04
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_6291_t04
Sample SD_6291_t04 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 7.805672034
7896746 8.347994686
7896748 4.611252438
7896750 4.525403617
7896752 8.681179133
7896817 6.809310224
7896878 5.596200356
7897006 5.102923375
7897068 6.880033921
7897078 7.844205386
7897119 5.722513103
7897172 7.419024037
7897236 6.167877476
7897288 5.380816899
7897305 5.506189609
7897370 8.148679446
7897404 7.999241
7897482 7.119389035
7897522 7.6429308
7897527 7.411422311

Total number of rows: 8454

Table truncated, full table size 164 Kbytes.




Supplementary file Size Download File type/resource
GSM2599907_6291t4_062112_HuGene-1_0-st-v1_.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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