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Sample GSM2600073 Query DataSets for GSM2600073
Status Public on Apr 10, 2018
Title Sleep deprived subject 6207 blood collection 10 [D8]
Sample type RNA
 
Source name blood
Organism Homo sapiens
Characteristics subject id: s6207
fatigue_category: susceptible
subject group: Sleep Deprived
study phase: experimental
timepoint: t07
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_6207_t10
Reanalysis of sample SD_6207_t10 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 7.169219635
7896746 9.075803703
7896748 5.655517047
7896750 4.299066292
7896752 8.457007774
7896817 6.17220585
7896878 5.992262129
7897006 5.686151794
7897068 7.267451187
7897078 7.649915262
7897119 6.198087252
7897172 7.366696027
7897236 6.551299117
7897288 6.002540489
7897305 5.643929487
7897370 7.861237987
7897404 7.434616846
7897482 7.277427663
7897522 6.621953538
7897527 7.434636505

Total number of rows: 8397

Table truncated, full table size 163 Kbytes.




Supplementary file Size Download File type/resource
GSM2600073_6207t10_HuGene-1_0-st-v1_.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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