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Sample GSM34713 Query DataSets for GSM34713
Status Public on Nov 09, 2004
Title Dog1 Left Lung (Injured) Base NonDependent
Sample type RNA
 
Source name dog lungs
Organism Canis lupus familiaris
Extracted molecule total RNA
 
Description 3 mongrel dogs (weight 21.3±1.5 kg) were anesthetized with 25 mk/kg pentobarbital i.v. and instrumented with femoral arterial and venous catheters. Anesthesia was maintained with additional pentobarbital (5 mg/kg iv every hour and when indicated) and muscle relaxation provided by pancuronium (3 mg bolus and 0.5 mg hourly iv). A 39 or
41 french double-lumen endobronchial tube was placed via a tracheostomy and position confirmed by fiberoptic bronchoscopy. The animals were ventilated with a “dual piston” large animal ventilator, permitting independent control of tidal volume (Vt), inspired oxygen fraction (FiO2), and positive end-expiratory pressure (PEEP), and measurement of airway opening pressure (Paw) and end-tidal partial pressure of carbon dioxide (ETPCO2) for each lung. Oxygen saturation (SaO2) was continuously measured using a pulse oximeter applied to the tongue or ear and ETPCO2, arterial blood pressure (Pa), Paw, and esophageal pressure (Pes) were continuously recorded. An infusion of lactated ringers (LR, 5-10 ml/kg/hr) was given for maintenance fluid replacement. Rectal or PA temperature was maintained at 36±1?C with radiant heat lamps. At the conclusion of the study, the animals were sacrificed by exsanguination after supplemental pentobarbital (10 mg/kg i.v.). After instrumentation, the individual lung Vt !Sample_description =were adjusted to provide an ETPCO2 of 30-35 mmHg at a respiratory rate of 25 breaths/min. The left lung was then mildly injured by repeated lavage with warmed saline, 20 ml/kg repeated 4 times. Ventilation continued at baseline settings, with the addition of 5 cm H2O PEEP to the control right lung, for 5 hours. At that time the animal was sacrificed by exsanguination, the chest opened, and 10 tissue samples taken from 5 corresponding
regions in both lungs (apex- dependent and non-dependent, base- non dependent, mid, and dependent). The lung tissue samples were immersed in RNAlater (Ambion, Austin, Texas) and frozen for subsequent analysis. In some animals, additional tissue samples were taken and stored in 10% formalin for immunohistochemistry.
Sample_hybridization: total RNA was converted to first-strand cDNA using a hybrid reverse transcription primer consisting of oligo-dT and T7 RNA polymerase promoter sequences. The single-stranded cDNA was then converted to double-stranded cDNA. Complementary DNA corresponding to 5-10 µg of total RNA was used in a cRNA amplification step using T7 RNA polymerase and two biotinylated nucleotide precursors. The resulting biotinylated cRNA was fragmented to a size of approximately 50 bp, and approximately 20-30 µg of the biotinylated cRNA was hybridized to the Human HG_U133A GeneChip (Affymetrix, Santa Clara, CA). The bound cRNA was visualized by binding of streptavidin/phycoerythrin conjugates to the hybridized GeneChip, followed by laser scanning of bound phycoerythrin.
Sample_RNA_Isolation: Tissues (~50 mg) were taken frozen and directly solubilized in chaotropic solubilization buffer using a Brinkman Polytron tissue disruptor. Larger tissue fragments (>100mg) were pulverized into frozen powder with a mortar and pestle, pre-chilled to liquid nitrogen temperature, and then the frozen powder was solubilized with the Polytron. RNA was purified using Trizol LS (Life Technologies) and an additional RNA purification step was conducted using the RNAeasy purification kit (Qiagen Inc., Valencia, CA). Approximately 10 µg of purified, total RNA was used for analyses.
Sample_strain: Mongrel
Keywords = unilateral canine lung injury model, microarray, gene expression, mechanical ventilation
 
Submission date Nov 05, 2004
Last update date Oct 28, 2005
Contact name Shwu-Fan Ma
E-mail(s) sma1@jhmi.edu
Phone 410-550-5996
Organization name Johns Hopkins University
Street address 5501 Hopkins Bayview Circle
City Baltimore
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL96
Series (1)
GSE1935 PGA_DogLung_regional_MV

Data table header descriptions
ID_REF
VALUE 'signal' a measure of the abundance of a transcript
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or A (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 332.1 P 0.003595
AFFX-BioB-M_at 702.4 P 0.000127
AFFX-BioB-3_at 204.3 P 0.000509
AFFX-BioC-5_at 907.9 P 0.00011
AFFX-BioC-3_at 820.5 P 0.000297
AFFX-BioDn-5_at 544.7 P 0.00006
AFFX-BioDn-3_at 5296.4 P 0.00011
AFFX-CreX-5_at 6752.8 P 0.000044
AFFX-CreX-3_at 11222.7 P 0.000044
AFFX-DapX-5_at 26.2 A 0.262827
AFFX-DapX-M_at 46.3 P 0.021902
AFFX-DapX-3_at 2.9 A 0.949771
AFFX-LysX-5_at 15 A 0.470241
AFFX-LysX-M_at 51.9 A 0.455413
AFFX-LysX-3_at 7.6 A 0.58862
AFFX-PheX-5_at 6 A 0.814869
AFFX-PheX-M_at 5.2 A 0.804734
AFFX-PheX-3_at 17 A 0.712257
AFFX-ThrX-5_at 6.2 A 0.794268
AFFX-ThrX-M_at 21.4 A 0.340661

Total number of rows: 22283

Table truncated, full table size 580 Kbytes.




Supplementary file Size Download File type/resource
GSM34713.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM34713.EXP.gz 258 b (ftp)(http) EXP
GSM34713.rpt.gz 1.2 Kb (ftp)(http) RPT
GSM34713.txt.gz 143.7 Kb (ftp)(http) TXT

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