NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1006637 Query DataSets for GSM1006637
Status Public on Sep 19, 2013
Title RJ7-5
Sample type RNA
 
Source name lung
Organism Mus musculus
Characteristics tissue: lung
genotype: wild type
age: 8–12 weeks old
gender: male
background strain: C57BL/6
treatment: 10% O2
Treatment protocol For gene expression study, PMVEC cells were treated with recombinant IL-4 (rIL-4, 50 ng/mL, Sigma-Aldrich), or vehicle control for 24h (n=3).
Growth protocol WT and IL-4 KO (C57BL/6 background; male, 8–12 weeks old) were were placed in a Plexiglas chamber maintained at 10% O2 (hypoxic group) or in a chamber open to room air (normoxic group) for 4 days (d) with a 12:12-hours (h) light-dark cycle. After exposure to hypoxia or normoxia, mice were sacrificed and the lungs were harvested for RNA extraction. Mouse PMVEC were isolated from 4–6-week-old female C57BL/6 mice. Cells were incubated at 37°C in a humidified atmosphere of 5% CO2 and were used at passages 3–5.
Extracted molecule total RNA
Extraction protocol Total lung RNA was isolated from each animal or from PMVEC and extracted using the Trizol Reagent method (Invitrogen). Additional purification was performed on RNAeasy columns (Qiagen, Valencia, CA). The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol Total RNA was labled with the Ambion TotalPrep RNA Amplification Kit according to manufacturers suggested protocols.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description hypoxia
Data processing A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction. The expression values for all the probes for each sample were scaled to have median 256 (2^8) and then log (base 2) transformed before performing statistical analysis.
 
Submission date Sep 19, 2012
Last update date Sep 19, 2013
Contact name chris cheadle
E-mail(s) ccheadl1@jhmi.edu
Phone 4105505984
Organization name JHU
Department SOM
Lab JHBMC Genomics Core
Street address 5200 Eastern Ave
City baltimore
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL6885
Series (1)
GSE40999 Th2 cytokine IL-4 is critical in initiating pulmonary vascular inflammation under hypoxic conditions and induces pulmonary vascular endothelial cell activation.

Data table header descriptions
ID_REF
VALUE log2 median normalized scaled intensity value
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 8.68 0.0000
ILMN_1212612 7.85 0.0000
ILMN_1212619 7.76 0.0000
ILMN_1212628 7.14 0.3252
ILMN_1212632 7.16 0.2967
ILMN_1212636 11.76 0.0000
ILMN_1212637 11.76 0.0000
ILMN_1212645 7.03 0.4810
ILMN_1212648 9.08 0.0000
ILMN_1212653 10.61 0.0000
ILMN_1212672 8.21 0.0000
ILMN_1212682 7.28 0.1802
ILMN_1212683 8.48 0.0000
ILMN_1212685 6.84 0.8252
ILMN_1212692 8.44 0.0000
ILMN_1212693 9.52 0.0000
ILMN_1212695 6.91 0.6951
ILMN_1212698 6.79 0.8835
ILMN_1212702 16.15 0.0000
ILMN_1212703 8.94 0.0000

Total number of rows: 25697

Table truncated, full table size 630 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap