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Sample GSM2600090 Query DataSets for GSM2600090
Status Public on Apr 10, 2018
Title Sleep deprived subject 6234 blood collection 03 [D8]
Sample type RNA
 
Source name blood
Organism Homo sapiens
Characteristics subject id: s6234
fatigue_category: susceptible
subject group: Sleep Deprived
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 SD_6234_t03
Reanalysis of sample SD_6234_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. 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 7.30464306
7896746 9.710296794
7896748 6.86575297
7896750 6.780798762
7896752 10.12580501
7896817 8.221945417
7896878 5.636607917
7897006 5.745437723
7897068 6.725196529
7897078 7.80525901
7897119 6.375243973
7897172 7.308277993
7897236 6.516737884
7897288 5.657454009
7897305 5.456341446
7897370 7.950610171
7897404 7.986618407
7897482 6.727240708
7897522 7.086785123
7897527 6.916205429

Total number of rows: 8397

Table truncated, full table size 163 Kbytes.




Supplementary file Size Download File type/resource
GSM2600090_6234t3_C_060812_HuGene-1_0-st-v1_.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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