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Sample GSM1260255 Query DataSets for GSM1260255
Status Public on Apr 24, 2014
Title Non-Braindead HT_rep 34
Sample type RNA
 
Source name Lung biopsy of a non-braindead rat ventilated with HT method
Organism Rattus norvegicus
Characteristics stain: Wistar
gender: male
age: adult
brain status: no brain damage (NBD)
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 NBD_HT_34
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 10.4979004
100036765_at 9.26172686
100049583_at 10.7900461
100124593_at 9.73565334
100125361_at 7.41457954
100125362_at 8.41398065
100125364_at 9.96073807
100125365_at 10.4578612
100125367_at 8.30943271
100125368_at 9.05894168
100125369_at 7.58709184
100125370_at 12.0708464
100125372_at 8.00985399
100125373_at 10.9868918
100125374_at 9.04865075
100125377_at 7.12788965
100125384_at 7.5410418
100125385_at 9.64651431
100125386_at 7.45536862
100125595_at 7.94153244

Total number of rows: 19239

Table truncated, full table size 391 Kbytes.




Supplementary file Size Download File type/resource
GSM1260255_Yard_211210_II_34_RaGene-1_0-st-v1_.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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