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Sample GSM2600104 Query DataSets for GSM2600104
Status Public on Apr 10, 2018
Title Sleep deprived subject 6291 blood collection 09 [D8]
Sample type RNA
 
Source name blood
Organism Homo sapiens
Characteristics subject id: s6291
fatigue_category: susceptible
subject group: Sleep Deprived
study phase: experimental
timepoint: t06
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_t09
Reanalysis of sample SD_6291_t09 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.
 
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

Data table header descriptions
ID_REF
VALUE RMA log2 expression

Data table
ID_REF VALUE
7896742 7.704382279
7896746 7.7099143
7896748 4.685007919
7896750 3.771977514
7896752 8.022084398
7896817 7.402844133
7896878 5.561242942
7897006 5.530989007
7897068 6.609375315
7897078 8.090110632
7897119 5.793077676
7897172 7.261642973
7897236 6.262421794
7897288 4.959971923
7897305 5.899301777
7897370 8.029323027
7897404 8.301747432
7897482 6.770987886
7897522 7.786352191
7897527 7.087301708

Total number of rows: 8397

Table truncated, full table size 163 Kbytes.




Supplementary file Size Download File type/resource
GSM2600104_6291t9_061412_HuGene-1_0-st-v1_.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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