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Sample GSM2599824 Query DataSets for GSM2599824
Status Public on Apr 10, 2018
Title Control subject 6297 blood collection 03 [D6]
Sample type RNA
 
Source name blood
Organism Homo sapiens
Characteristics subject id: s6297
fatigue_category: unknown
subject group: Control
study phase: baseline
timepoint: t03
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_t03
Sample C_6297_t03 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 7.142422204
7896746 8.404808675
7896748 6.104650941
7896750 4.397694093
7896752 8.534760146
7896817 6.741209752
7896878 5.970706828
7897006 5.680593074
7897068 6.935424646
7897078 7.872038521
7897119 6.172077487
7897172 7.249332921
7897236 6.215730418
7897288 5.244329192
7897305 5.833135322
7897370 8.071762198
7897404 7.934233642
7897482 7.159110661
7897522 7.661244495
7897527 7.13695438

Total number of rows: 8454

Table truncated, full table size 164 Kbytes.




Supplementary file Size Download File type/resource
GSM2599824_6297t3_2_071012_HuGene-1_0-st-v1_.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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