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Sample GSM1378013 Query DataSets for GSM1378013
Status Public on May 03, 2014
Title 437_CreER: mutant mouse 3
Sample type RNA
 
Source name mouse lung, tamoxifen-treated Tmem1002loxP/2loxP;ROSA26+/CreER
Organism Mus musculus
Characteristics tissue: lung
genotype/variation: Tmem1002loxP/2loxP;ROSA26+/CreER
Treatment protocol Three control mice and three mutant mice were treated with tamoxifen (two consecutive intraperitoneal injections, 0.1 mg/g of body weight) to activate CreER recombinase.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).
Label biotin
Label protocol Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).
 
Hybridization protocol 750 ng of labeled cRNA samples were hybridized to each mouse-8 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA). Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual.
Scan protocol Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions.
Data processing The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer(Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4)). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected gene signal value was transformed by logarithm and normalized by quantile method. The comparative analysis between test sample and control sample was carried out using fold-change. Go-ontology analysis for significant probe list was performed using PANTHER (http://www.pantherdb.org/panther/ontologies.jsp), using text files containing Gene ID list and accession number of illumina probe ID. All data analysis and visualization of differentially expressed genes was conducted using R 2.4.1(www.r-project.org).
 
Submission date May 02, 2014
Last update date May 03, 2014
Contact name Young Jae Lee
E-mail(s) copg2@hanmail.net
Organization name Gachon University
Department Lee Gil Ya cancer and Diabetes Institute
Lab Developmental Genetics
Street address 155, Gaetbeol-ro, Yeonsu-gu
City Incheon
ZIP/Postal code 406-840
Country South Korea
 
Platform ID GPL6885
Series (1)
GSE57256 Expression data from adult lungs isolated from TMEM100-deficient mice

Data table header descriptions
ID_REF
VALUE normalized probe intensity, log2 based
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212612 8.915946434 0
ILMN_1212619 8.457522525 0.03132832
ILMN_1212632 8.715781428 0.002506266
ILMN_1212636 11.83228629 0
ILMN_1212637 10.07639154 0
ILMN_1212648 10.28155627 0
ILMN_1212653 9.63946686 0
ILMN_1212672 9.661623356 0
ILMN_1212692 10.67283668 0
ILMN_1212693 10.00846015 0
ILMN_1212702 10.3811844 0
ILMN_1212703 8.757724849 0.002506266
ILMN_1212717 8.611211764 0.005012531
ILMN_1212720 8.838353198 0
ILMN_1212759 9.723605765 0
ILMN_1212794 9.745155444 0
ILMN_1212835 8.706838909 0.002506266
ILMN_1212875 9.482549312 0
ILMN_1212894 11.32031501 0
ILMN_1212902 9.847148549 0

Total number of rows: 13261

Table truncated, full table size 380 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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