|
| Status |
Public on May 08, 2018 |
| Title |
PBMC_NightOrientedSchedule_RelTime_30.3_Subject_T23 |
| Sample type |
RNA |
| |
|
| Source name |
PBMC_NightOrientedSchedule_RelTime_30.3
|
| Organism |
Homo sapiens |
| Characteristics |
subject: T23
condition: NightOrientedSchedule
relclocktime: 30.3
|
| 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 30.3 h after habitual wake time during night-oriented schedule in Subject T23
|
| 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 |
GSM3484196 |
