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Sample GSM2870771 Query DataSets for GSM2870771
Status Public on May 08, 2018
Title PBMC_NightOrientedSchedule_RelTime_38.3_Subject_T21
Sample type RNA
 
Source name PBMC_NightOrientedSchedule_RelTime_38.3
Organism Homo sapiens
Characteristics subject: T21
condition: NightOrientedSchedule
relclocktime: 38.3
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 38.3 h after habitual wake time during night-oriented schedule in Subject T21
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 GSM3484177

Data table header descriptions
ID_REF
VALUE RMA normalized log2 intensity signal

Data table
ID_REF VALUE
23064070 9.288920608
23064071 7.507403459
23064072 8.07540979
23064073 7.011570753
23064074 3.764244661
23064075 9.017805176
23064076 6.180109744
23064077 6.591782628
23064078 7.66185015
23064079 4.111180158
23064080 11.79046086
23064081 4.264742994
23064083 4.8106016
23064084 3.013537699
23064085 5.171063991
23064086 4.750361077
23064087 4.362341396
23064088 4.749293328
23064089 3.577870134
23064090 4.777368672

Total number of rows: 26943

Table truncated, full table size 784 Kbytes.




Supplementary file Size Download File type/resource
GSM2870771_DBN180.CEL.gz 1.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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