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Sample GSM29709 Query DataSets for GSM29709
Status Public on Oct 26, 2004
Title VehLPS1
Sample type RNA
 
Source name murine lungs
Organism Mus musculus
Extracted molecule total RNA
 
Description Mice treated with 2.5ug/kg LPS intratracheally, samples at 24hr. Mice given simvastatin 20mg/kg for 48 hr prior to sample collection (2 doses of simvastatin).
Sample_age: 7-8 weeks old
Sample_hybridization: total RNA was converted to first-strand cDNA using a hybrid reverse transcription primer consisting of oligo-dT and T7 RNA polymerase promoter sequences. The single-stranded cDNA was then converted to double-stranded cDNA. Complementary DNA corresponding to 5-10 µg of total RNA was used in a cRNA amplification step using T7 RNA polymerase and two biotinylated nucleotide precursors. The resulting biotinylated cRNA was fragmented to a size of approximately 50 bp, and approximately 20-30 µg of the biotinylated cRNA was hybridized to the Mouse430 2.0 GeneChip (Affymetrix, Santa Clara, CA). The bound cRNA was visualized by binding of streptavidin/phycoerythrin conjugates to the hybridized GeneChip, followed by laser scanning of bound phycoerythrin.
Sample_RNA_Isolation: Tissues (~50 mg) were taken frozen and directly solubilized in chaotropic solubilization buffer using a Brinkman Polytron tissue disruptor. Larger tissue fragments (>100mg) were pulverized into frozen powder with a mortar and pestle, pre-chilled to liquid nitrogen temperature, and then the frozen powder was solubilized with the Polytron. RNA was purified using Trizol LS (Life Technologies) and an additional RNA purification step was conducted using the RNAeasy purification kit (Qiagen Inc., Valencia, CA). Approximately 10 µg of purified, total RNA was used for analyses.
Sample_sex: male
Sample_strain: C57BL6
Keywords = Murine, endothelial cell barrier function, inflammation, Simvastatin, LPS
 
Submission date Aug 31, 2004
Last update date Aug 28, 2018
Contact name Shwu-Fan Ma
E-mail(s) sma1@jhmi.edu
Phone 410-550-5996
Organization name Johns Hopkins University
Street address 5501 Hopkins Bayview Circle
City Baltimore
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL1261
Series (1)
GSE1871 SCCOR_MouseLung_Simva_LPS
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE 'signal' a measure of the abundance of a transcript
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 65.1 P 0.00762
AFFX-BioB-M_at 87 P 0.000258
AFFX-BioB-3_at 50.6 P 0.002023
AFFX-BioC-5_at 148 P 0.00011
AFFX-BioC-3_at 133.8 P 0.00007
AFFX-BioDn-5_at 181 P 0.00006
AFFX-BioDn-3_at 817.6 P 0.00039
AFFX-CreX-5_at 2437.1 P 0.00006
AFFX-CreX-3_at 2818 P 0.000044
AFFX-DapX-5_at 4.5 A 0.147939
AFFX-DapX-M_at 5.3 A 0.327065
AFFX-DapX-3_at 0.9 A 0.904333
AFFX-LysX-5_at 0.6 A 0.559359
AFFX-LysX-M_at 1.9 A 0.804734
AFFX-LysX-3_at 6.6 A 0.095667
AFFX-PheX-5_at 0.6 A 0.945848
AFFX-PheX-M_at 0.7 A 0.9273
AFFX-PheX-3_at 8 A 0.425962
AFFX-ThrX-5_at 1.5 A 0.686277
AFFX-ThrX-M_at 1.5 A 0.559354

Total number of rows: 45101

Table truncated, full table size 1199 Kbytes.




Supplementary file Size Download File type/resource
GSM29709.CEL.gz 6.6 Mb (ftp)(http) CEL
GSM29709.EXP.gz 267 b (ftp)(http) EXP
GSM29709.RPT.gz 1.1 Kb (ftp)(http) RPT
GSM29709.txt.gz 2.4 Mb (ftp)(http) TXT
Raw data provided as supplementary file

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