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Series GSE59404 Query DataSets for GSE59404
Status Public on Jul 16, 2014
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 #2 was to compare circadian gene expression in healthy lungs (samples labeled with the prefix “NT”) to lungs derived from endotoxemic animals (samples labeled with the prefix “LT”). For Microarray Experiment #2, 94 mice were placed under constant light conditions (LL 12:12, food ad libitum) at CT12 the prior day (7:00 PM local time). At CT10 (5:00 PM) on the day of the experiment a sub-group of 40 mice received a single intraperitoneal injection of 12 mg/kg E. coli O127:B8 endotoxin (LPS, Sigma L3129, Lot 029K4055), and sample collection began directly after. 3-4 mice per group were sacrificed at consecutive 4 hour intervals for 2-3 days. The left lung and the right upper lobe were frozen immediately in liquid nitrogen for microarray analysis. 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 #2 at the Channing Division of Network Medicine (Brigham and Women’s Hospital). Two biological samples (NT00L1 and LT00L1) were represented by 2 technical replicates on the microarray. The remaining biological samples were represented by a single technical replicate.
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
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 (112)
GSM1436369 ST-01012986_S-001146717_8450989018_A
GSM1436370 ST-01012989_S-001146730_8450989018_B
GSM1436371 ST-01013009_S-001146783_8450989018_C
This SubSeries is part of SuperSeries:
BioProject PRJNA255325

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
GSE59404_RAW.tar 3.1 Mb (http)(custom) TAR
Raw data included within Sample table
Processed data included within Sample table

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