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Sample GSM2599899 Query DataSets for GSM2599899
Status Public on Apr 10, 2018
Title Sleep deprived subject 6234 blood collection 11 [D6]
Sample type RNA
 
Source name blood
Organism Homo sapiens
Characteristics subject id: s6234
fatigue_category: susceptible
subject group: Sleep Deprived
study phase: experimental
timepoint: t08
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_6234_t11
Sample SD_6234_t11 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 7.134203048
7896746 8.617856429
7896748 5.603664334
7896750 4.774530886
7896752 8.92372812
7896817 8.781106249
7896878 5.931086423
7897006 5.630502565
7897068 6.820060002
7897078 7.902553229
7897119 6.231157831
7897172 7.435878269
7897236 6.483097917
7897288 5.658982446
7897305 5.890506954
7897370 7.797775143
7897404 7.890590707
7897482 7.140478551
7897522 6.640869964
7897527 6.767408639

Total number of rows: 8454

Table truncated, full table size 164 Kbytes.




Supplementary file Size Download File type/resource
GSM2599899_6234t11_HuGene-1_0-st-v1_.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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