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Sample GSM2599990 Query DataSets for GSM2599990
Status Public on Apr 10, 2018
Title Control subject 6089 blood collection 09 [D8]
Sample type RNA
 
Source name blood
Organism Homo sapiens
Characteristics subject id: s6089
fatigue_category: unknown
subject group: Control
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 C_6089_t09
Reanalysis of sample C_6089_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 7.586959642
7896746 8.960712149
7896748 5.927829566
7896750 5.514907797
7896752 9.282868933
7896817 6.623694372
7896878 5.728828046
7897006 5.75896737
7897068 6.876794508
7897078 7.998822576
7897119 6.211204287
7897172 7.546885547
7897236 6.495322611
7897288 5.220432833
7897305 5.738343447
7897370 7.937040315
7897404 7.981173075
7897482 6.915798309
7897522 7.921034988
7897527 7.278219202

Total number of rows: 8397

Table truncated, full table size 163 Kbytes.




Supplementary file Size Download File type/resource
GSM2599990_6089t9_re_013013_HuGene-1_0-st-v1_.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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