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Sample GSM585934 Query DataSets for GSM585934
Status Public on Dec 01, 2011
Title Fra2/tg_14 wk_lung_rep1
Sample type RNA
 
Channel 1
Source name fra-2 transgenic, 14 weeks
Organism Mus musculus
Characteristics background: C57BL6 x CBA
genotype: fra-2 (Fosl-2 gene) transgenic
gender: male
age: 14 weeks
tissue: lung
mouse id: 30157347
Extracted molecule total RNA
Extraction protocol Total RNA was isolated just before processing for expression profiling. For preparation of total RNA, individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).
Label Cy5
Label protocol For labeling, 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according to the TIGR protocol (Hegde P, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562).
 
Channel 2
Source name wild type pool, 14 weeks
Organism Mus musculus
Characteristics background: C57BL6 x CBA
genotype: wild type
gender: male
age: 14 weeks
tissue: lung
mouse id: 30157346, 30157590, 30157591, 30157593
Extracted molecule total RNA
Extraction protocol Total RNA was isolated just before processing for expression profiling. For preparation of total RNA, individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).
Label Cy3
Label protocol For labeling, 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according to the TIGR protocol (Hegde P, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562).
 
 
Hybridization protocol Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution labeled with the second dye. This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization, slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying, slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2.

Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597.
Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500.
Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10.
Scan protocol Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA).

Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500.
Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10.
Data processing Normalisation with GenePix Pro 6.1: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation.
 
Submission date Aug 23, 2010
Last update date Dec 01, 2011
Contact name Martin Irmler
Organization name Helmholtz Zentrum München GmbH
Department Institute of Experimental Genetics
Lab Gene Regulation & Epigenetics
Street address Ingolstaedter Landstrasse 1
City Neuherberg
State/province Bayern
ZIP/Postal code 85764
Country Germany
 
Platform ID GPL4937
Series (1)
GSE23745 Expression profiling of lung tissue from 6-, 10- and 14-week-old Fra2 transgenic male mice

Data table header descriptions
ID_REF
VALUE Normalised log2 ratio (Cy5/Cy3)

Data table
ID_REF VALUE
1 0.087
2 0.081
3 0.028
4 0.147
5 -0.172
6 0.113
7 0.045
8 0.190
9 0.017
10 -0.008
11 0.054
12 -0.028
13 -0.108
14 -0.427
15 -0.155
16 -0.131
17 -0.135
18 0.402
19 -0.168
20 0.546

Total number of rows: 20794

Table truncated, full table size 243 Kbytes.




Supplementary file Size Download File type/resource
GSM585934.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table

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