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Sample GSM930485 Query DataSets for GSM930485
Status Public on May 12, 2012
Title Muscle_AQM_5-8d_unloaded_UU43
Sample type RNA
 
Source name gastrocnemius muscle, treated with non-depolarizing NMBA and mechanically ventilated, 5d to 8d group, unloaded leg
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
gender: female
tissue: gactrocnemius muscle
treatment_1: non-depolarizing neuromuscular blocking agent (NMBA)
treatment_2: no loading
time: 5-8 days
Treatment protocol Briefly, the following surgery and instrumentation was completed with sterile technique: 1) Precordial silver wire electrocardiogram (ECG) electrodes were implanted subcutaneously. 2) An aortic catheter (28-gauge Teflon) was inserted via the left carotid artery to record arterial blood pressure. 3) A 0.9-mm Renathane catheter was threaded into the left jugular vein to administer parental solutions. 4) Three subcutaneous EEG needle electrodes were placed into the skull above the right and left temporal lobes, and a third reference electrode was placed in the neck region. 5) Temperature was measured by a vaginal thermistor and servo-regulated at 37°C. 6) A silicone cannula was inserted in the urethra to continuously record urine output.
During surgery or any possible irritating manipulation, the anesthetic isoflurane level was at >1.5%, which maintained the following states: 1) the electroencephalogram (EEG) was synchronized and dominated by high-voltage slow-wave activity; 2) mean arterial pressure was 100 mmHg, the heart rate, 420 beats/min, and 3) there were no evident EEG, blood pressure or heart rate responses to surgical manipulation. Isoflurane was delivered into the inspiratory gas stream by a precision mass-flow controller. After the initial surgery, Isoflurane was gradually lowered (over 1-2 days) and maintained at <0.5% during the remaining experimental period. Rats were ventilated through a per os coaxial tracheal cannula at 72 breaths/min with an inspiratory and expiratory ratio of 1:2 and a minute volume of 180–200 ml and gas concentrations of 50% O2, 47% N2, and 3% CO2, delivered by a precision volumetric respirator. Intermittent respiratory hyperinflations (6 per hour at 15 cmH2O), positive end-expiratory pressure (1.5 cmH2O), and expiratory CO2 monitoring were continuous. Neuromuscular blockade (NMBA) was induced on the first day (100 µg iv. alpha-cobrotoxin) and maintained by continuous infusion (250 µg/day, iv). Mechanical ventilation was initiated immediately after the NMBA induction. The left leg of the animal was activated for 6 hours at the shortest duration and 12 hours per day at durations 12 hours and longer throughout the experiment, using a mechanical lever arm that produced a continuous passive maximal ankle joint flexions-extensions at a speed of 13.3 cycles per minute. Gastrocnemius muscles were dissected from the loaded left leg and the unloaded right leg immediately after euthanasia.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted according to the standard Affymetrix protocol including Trizol extraction and RNeasy column cleanup.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 g total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000.
Description Experimental rat ICU model. AQM.
Unloaded leg.
UU43_100216
Data processing Analyses of the gene expression data were carried out in the freely available statistical computing language R using packages available from the Bioconductor project. The raw data were normalized using the robust multi-array average (RMA), background-adjusted, and log-transformed summarized values as first suggested by Li and Wong in 2001.
 
Submission date May 11, 2012
Last update date May 12, 2012
Contact name Monica Llano-Diez
Organization name Uppsala university
Department Neuroscience
Lab Clinical neurophysilogy
Street address Akademiska sjukhuset, Ing.85, 3tr
City Uppsala
ZIP/Postal code 75185
Country Sweden
 
Platform ID GPL6247
Series (1)
GSE37944 Sparing of muscle mass and function by passive loading in an experimental intensive care unit model

Data table header descriptions
ID_REF
VALUE RMA-calculated signal intensity

Data table
ID_REF VALUE
10815663 6.324787
10802023 5.270265
10799346 7.03537
10855114 2.755258
10872098 9.634478
10852144 8.213737
10803947 6.697178
10717233 7.772707
10908776 4.902212
10749874 10.30161
10822348 6.849996
10858275 6.080542
10833152 6.089613
10752405 5.597504
10841806 6.78883
10881109 9.00813
10742927 3.610041
10939435 7.39359
10721875 5.051476
10909080 6.519588

Total number of rows: 26208

Table truncated, full table size 457 Kbytes.




Supplementary file Size Download File type/resource
GSM930485_PA079_UU43_100216_RaGene-1_0-st-v1_.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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