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Series GSE59396 Query DataSets for GSE59396
Status Public on Jul 16, 2014
Title CIRCADIAN RHYTHM REPROGRAMMING DURING LUNG INFLAMMATION/ Microarray Experiment #1
Organism Mus musculus
Experiment type Expression profiling by array
Summary In this study we utilized a genome-wide approach to analyze circadian patterns of gene expression in mouse lung lungs, both in the basal state and in the setting of systemic inflammation caused by endotoxemia. We chose the lung because it represents a primary portal for systemic infection and organ failure in critically ill patients, and because the lung exhibits strong physiological circadian rhythms in health and in diseases such as asthma. The gene expression the data presented here was correlated to histological observations and metabolite measurements derived from the same biological samples, in order to obtain a broad picture of how inflammation impacts circadian rhythms in mouse lung.
 
Overall design To examine circadian regulation in mouse lung we performed 2 independent time-series experiments (Microarray Experiments #1 and #2), in which groups of mice were euthanized at 4 hour intervals for 48 hours. The purpose of Microarray Experiment #1 was to control for environmental influences (light and nutrition) on the detection of circadian rhythms in gene expression. In Microarray Experiment #1, 72 mice were segregated equally into 2 equal groups the day prior to the experiment at the beginning of the dark phase (Circadian Time 12 (CT12) or 7:00 PM local time). In one group (samples labeled with the suffix “MR”) the mice were kept under standard lighting and nutritional conditions (LD 12:12). In the second group (samples labeled with the suffix “DD”), mice were kept in constant darkness and food pellets were removed from their cages at the start of sample acquisition (DD 12:12+STV). Sample acquisition commenced at CT4 (or 11:00 AM local time). For each group 3 animals were sacrificed per time point (12 time points total). For mRNA isolation lung tissue was immersed in RNAlater (Qiagen) and total RNA was then extracted using the RNeasy Mini Kit (Qiagen). RNA quality (RIN>=7) was confirmed using an Agilent 2100 Bioanalyzer. RNA from all biological samples was labeled at once using the Ambion TotalPrep-96 RNA Amplification Kit. The samples were then blinded, randomized to chip position and hybridized to the Illumina MouseRef-8 v2.0 Expression BeadChips. For Microarray Experiment #1 RNA labeling and microarray hybridization were conducted at the Partners Center for Personalized Genetic Medicine. All biological samples were represented by a single technical replicate on the microarray.
 
Contributor(s) Haspel J, Chettimada S, Shaik R, Chu J, Raby B, Cernadas M, Carey V, Process V, Hunninghake G, Ifedigbo E, Lederer J, Englert J, Pelton A, Coronata A, Fredenburgh L, Choi A
Citation(s) 25208554
Submission date Jul 14, 2014
Last update date Jun 14, 2018
Contact name Jen-hwa Chu
E-mail(s) jen-hwa.chu@yale.edu
Organization name Yale University School of Medicine
Department Pulmonary, Critical Care and Sleep Medicine
Street address PO Box 208057
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platforms (1)
GPL6885 Illumina MouseRef-8 v2.0 expression beadchip
Samples (80)
GSM1435584 T24L1MR
GSM1435585 T20L2DD
GSM1435586 T8L4MR
This SubSeries is part of SuperSeries:
GSE59444 CIRCADIAN RHYTHM REPROGRAMMING DURING LUNG INFLAMMATION
Relations
BioProject PRJNA255327

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE59396_RAW.tar 3.1 Mb (http)(custom) TAR
Raw data included within Sample table
Processed data included within Sample table

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