|
| Status |
Public on Feb 14, 2019 |
| Title |
PBMC_Control_DayOrientedSchedule_RelTime_12.3_Subject_T17 [re-analysis] |
| Sample type |
RNA |
| |
|
| Source name |
PBMC_DayOrientedSchedule_RelTime_12.3
|
| Organism |
Homo sapiens |
| Characteristics |
subject: T17
experimentalgroup: Control
condition: DayOrientedSchedule
relclocktime: 12.3
|
| 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 |
reanalysis of GSM2870728, PBMC sample taken at 12.3 h after habitual wake time during day-oriented schedule in Subject T17 in the Control group
|
| Data processing |
Affymetrix CEL files were normalized by RMA preprocessing methodology using the Oligo package (v1.38.0) in R (v3.4.1).
|
| |
|
| Submission date |
Nov 19, 2018 |
| Last update date |
Feb 16, 2019 |
| 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) |
| GSE122725 |
The phase-shifting effect of bright light exposure on circadian rhythmicity in the human transcriptome |
|
| Relations |
| Reanalysis of |
GSM2870728 |
