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Sample GSM2870726 Query DataSets for GSM2870726
Status Public on May 08, 2018
Title PBMC_DayOrientedSchedule_RelTime_4.2_Subject_T17
Sample type RNA
 
Source name PBMC_DayOrientedSchedule_RelTime_4.2
Organism Homo sapiens
Characteristics subject: T17
condition: DayOrientedSchedule
relclocktime: 4.2
Treatment protocol Peripheral blood mononuclear cells (PBMCs) were isolated by centrifugation for 30 minutes at 1600rpm on a density gradient (Histopaque-1077, Sigma Aldrich, Oakville, ON, Canada). PBMCs were washed 3 times in phosphate-buffered saline (PBS), lysed in TRIzol (Life Technologies, Burlington, ON, Canada) and stored at -80°C until further processing.
Growth protocol An indwelling catheter was inserted in a forearm vein at least 4 hours prior to the start of each 24-hour measurement period.
Extracted molecule total RNA
Extraction protocol Extraction of RNA was performed by addition of chloroform in order to separate organic and aqueous components. Isopropanol and subsequent ethanol washes were used to precipitate and purify the RNA. RNA was dissolved in RNase-free H2O (Qiagen, Toronto, ON, Canada). Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).
Label Biotin
Label protocol Sense-strand cDNA was synthesized from 10 ng of total RNA, and fragmentation and labeling were performed to produce ds-cDNA with the GeneChip® Pico Reagent Kit according to manufacturer’s instructions (ThermoFisher Scientific-Affymetrix).
 
Hybridization protocol After fragmentation and labeling, 2.8 µg DNA target was hybridized on Clariom™S HT, Human (ThermoFisher Scientific-Affymetrix).
Scan protocol Arrays were scanned on a Affymetrix GeneTitan instrument (ThermoFisher Scientific-Affymetrix) according to the manufacturer’s protocol.
Description PBMC sample taken at 4.2 h after habitual wake time during day-oriented schedule in Subject T17
Data processing Affymetrix CEL files were normalized by RMA preprocessing methodology using the Oligo package (v1.38.0) in R (v3.4.1). Probe sets were included in downstream analysis if they were expressed above background probe signal (mean + 2*SD) in at least 25% of the samples.
 
Submission date Nov 30, 2017
Last update date Nov 19, 2018
Contact name Laura Kervezee
E-mail(s) [email protected]
Organization name McGill University
Department Douglas Mental Health University Institute
Street address 6875 LaSalle Boulevard
City Montreal
State/province Quebec
ZIP/Postal code H4H 1R3
Country Canada
 
Platform ID GPL24324
Series (1)
GSE107537 The effect of simulated night shift work on the circadian regulation of the human transcriptome
Relations
Reanalyzed by GSM3484132

Data table header descriptions
ID_REF
VALUE RMA normalized log2 intensity signal

Data table
ID_REF VALUE
23064070 9.34071394
23064071 7.865524711
23064072 7.266782318
23064073 7.059196608
23064074 3.678039625
23064075 8.723242233
23064076 6.767056634
23064077 6.752425671
23064078 7.768181222
23064079 3.618439333
23064080 11.80956742
23064081 3.566600234
23064083 5.228834635
23064084 3.163867166
23064085 5.479689092
23064086 4.510282889
23064087 4.413313955
23064088 5.563639422
23064089 3.451150473
23064090 5.352322235

Total number of rows: 26943

Table truncated, full table size 784 Kbytes.




Supplementary file Size Download File type/resource
GSM2870726_DBN134.CEL.gz 1.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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