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Sample GSM1260270 Query DataSets for GSM1260270
Status Public on Apr 24, 2014
Title Braindead HT_rep 24
Sample type RNA
 
Source name Lung biopsy of a braindead rat ventilated with HT method
Organism Rattus norvegicus
Characteristics stain: Wistar
gender: male
age: adult
brain status: brain damage (BD)
ventilation type: high tidal volume ventilation (HT)
Extracted molecule total RNA
Extraction protocol Total RNA of right lung tissue was extracted using Trizol® Reagent (Invitrogen GmbH, Karslruhe, Germany). DNase treatment was carried out, using DNA Free Kit (Ambion / Life Technologies GmbH, Darmstadt). RNA yield, quality, and integrity were assessed by agarose gel electrophoresis and spectrophotometry. RNA concentration was assessed by 260/280 measurements using the Infinite® 200 PRO NanoQuant (Tecan Group Ltd., CH), and RNA integrity was measured by Agilent Bioanalyzer 2100 System (Agilent, Böblingen, Germany). 1 µg RNA was transcribed to cDNA according to the protocol provided with the High Capacity cDNA Reverse Transcription kit (Life Technologies GmbH, Darmstadt, Germany). Recombinant ribonuclease inhibitor was added to prevent RNase-mediated degradation.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
 
Hybridization protocol Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
Scan protocol Affymetrix GeneArray Scanner3000
Description BD_HT_24
Data processing The data were analyzed with a commercial software called JMP Genomics, version 5, from SAS. Gene expression profiling was performed using arrays of RaGene10stv1-type from Affymetrix. A Custom CDF Version 14 with entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.
 
Submission date Nov 06, 2013
Last update date Apr 25, 2014
Contact name Carsten Sticht
Organization name University Heidelberg
Department ZMF
Street address Theodor-Kutzer-Ufer
City Mannheim
ZIP/Postal code 68169
Country Germany
 
Platform ID GPL17896
Series (1)
GSE52142 Open lung approach with low tidal volume mechanical ventilation attenuates lung injury in rats with massive brain damage

Data table header descriptions
ID_REF
VALUE Quantile normalized signal intensity

Data table
ID_REF VALUE
100034253_at 10.3862947
100036765_at 9.47395206
100049583_at 11.640708
100124593_at 10.4672162
100125361_at 7.6059811
100125362_at 8.40010036
100125364_at 9.98201828
100125365_at 10.3225211
100125367_at 8.38420553
100125368_at 9.34874792
100125369_at 7.56698633
100125370_at 12.288615
100125372_at 8.02885378
100125373_at 11.8416253
100125374_at 9.13080354
100125377_at 7.01730603
100125384_at 7.37352722
100125385_at 9.57203795
100125386_at 7.59524404
100125595_at 7.72270951

Total number of rows: 19239

Table truncated, full table size 391 Kbytes.




Supplementary file Size Download File type/resource
GSM1260270_Yard_201210_IV_24_RaGene-1_0-st-v1_.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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