NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2599825 Query DataSets for GSM2599825
Status Public on Apr 10, 2018
Title Control subject 6297 blood collection 04 [D6]
Sample type RNA
 
Source name blood
Organism Homo sapiens
Characteristics subject id: s6297
fatigue_category: unknown
subject group: Control
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 C_6297_t04
Sample C_6297_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 7.824789431
7896746 8.292569282
7896748 5.794324248
7896750 4.439908703
7896752 8.404886041
7896817 7.034212845
7896878 5.81246807
7897006 5.683515711
7897068 6.76853773
7897078 8.104378924
7897119 6.234538184
7897172 7.569710371
7897236 6.020801837
7897288 5.213709014
7897305 5.882779035
7897370 8.120041615
7897404 8.264710912
7897482 7.111999726
7897522 8.140976707
7897527 7.177582965

Total number of rows: 8454

Table truncated, full table size 164 Kbytes.




Supplementary file Size Download File type/resource
GSM2599825_6297t4_re_013013_HuGene-1_0-st-v1_.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap