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Series GSE9400 Query DataSets for GSE9400
Status Public on Oct 10, 2009
Title Hypoxic gene regulation on mice Quadriceps muscle
Organism Mus musculus
Experiment type Expression profiling by array
Summary To address whether hypoxia contributes to muscle patho-physiology, normal, adult C57 mice were exposed to chronic, normobaric and hypobaric hypoxic environments for 2 weeks in order to simulate levels of hypoxaemia reported in DMD patients with advanced respiratory insufficiency. Control mice were maintained under normoxic conditions. Control and experimental mice were studied.
Keywords: Hypoxia effect, Comparison type
 
Overall design Adult male C57Bl/10 mice were used in experiments. At the beginning of the experiment mice were divided into two groups, control (room condition) and hypoxic (hypoxic condition), over a period of 2 weeks. The hypoxic group was gradually exposed to lower levels of hypoxia in an especially designed and hermetically closed hypoxic chamber. A Pegas 4000 MF(Columbus Instruments) gas blending system was used. The oxygen level was gradually decreased from 21% to 8% over one week and animals were kept at 8% oxygen for another 7 days. Animal’s weights were monitored daily. Food and water were changed daily for the time of the experiment. After two weeks animals were euthanized using CO2, Extensor digitorum longus (EDL) and Soleus muscles were dissected for physiological studies. Prior to physiological analysis each group was divided into two smaller groups (subgroups). In the first subgroup the primary focus on physiological muscle analysis was on (EDL) while in the other subgroup it was on Soleus. This division allowed us that both muscles, EDL and Soleus were analyzed at the same time after euthanization.
RNA isolation
Total RNA was isolated from each QF muscle by Tri-Reagent (Ambion, Austin, TX) as described by manufacturer. Isolated total RNA were cleaned up by RNeasy mini kit (Qiagen, Valencia, CA) as described by manufacturer. The purity and concentration of total RNA were determined by measurement of absorbance at 260 and 280nm using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). To satisfy our purity criteria, we discarded all RNA samples that did not have a 260/280 ratio between 1.8 and 2.1. To satisfy our criteria for integrity, we required that all RNA used in our experiments have single peaks for the 18S and 28S bands as determined by the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA).
Linear amplification and cRNA labeling
Three microliter total RNA was used for each sample to obtain linearly amplified labeled cRNA by using GeneChip® One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA) as manufacturer described. Briefly; total RNA was used to generate double-stranded cDNA with the T7-oligo (dT) primer. This double-stranded cDNA was used in vitro transcription and biotin labeling steps. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280nm. All the cRNA 260/280 ratios were between 1.9 and 2.1. Quality control (QC) of the labeled cRNA products was assessed by performing 1µg labeled cRNA on 2% agarose gel to see similar RNA smear type.
Fragmentation and microarray hybridization
Fifteen micrograms labeled cRNA of hypoxic or normoxic QF muscle was fragmented, and 10μg was hybridized to Affymetrix® Mouse 430 ver 2.0 GeneChip arrays for 18–24h (Affymetrix Inc.). Each microarray was washed and stained with streptavidin–phycoerythrin and scanned at a 6-μm resolution with Agilent model G2500A GeneArray scanner A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
 
Contributor(s) Budak MT, Willmann G, Bogdanovich S, Baby SM, Wiesen MH, Fu QM, Querfurth HW, Mosqueira M, Iturriaga R, Lahiri S, Khurana TS
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Submission date Oct 22, 2007
Last update date Feb 11, 2019
Contact name Murat T Budak
E-mail(s) mtbudak@mail.med.upenn.edu
Phone 215-8989726
Organization name University of Pennsylvania
Department
Lab Rubinstein and Khurana Labs
Street address
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (8)
GSM239142 Control-1
GSM239143 Control-2
GSM239144 Control-3
Relations
BioProject PRJNA103123

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
GSE9400_RAW.tar 31.8 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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