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Sample GSM29716 Query DataSets for GSM29716
Status Public on Oct 26, 2004
Title SimvaLPS2
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 103.1 P 0.002275
AFFX-BioB-M_at 188 P 0.00007
AFFX-BioB-3_at 86.9 P 0.000972
AFFX-BioC-5_at 258.8 P 0.00007
AFFX-BioC-3_at 212.8 P 0.000044
AFFX-BioDn-5_at 282.2 P 0.000052
AFFX-BioDn-3_at 1506.2 P 0.00011
AFFX-CreX-5_at 3894.4 P 0.000052
AFFX-CreX-3_at 4433.4 P 0.000044
AFFX-DapX-5_at 8.9 P 0.046482
AFFX-DapX-M_at 11.6 M 0.058444
AFFX-DapX-3_at 0.8 A 0.979987
AFFX-LysX-5_at 0.5 A 0.737173
AFFX-LysX-M_at 1.8 A 0.749204
AFFX-LysX-3_at 0.8 A 0.659339
AFFX-PheX-5_at 0.8 A 0.941556
AFFX-PheX-M_at 0.7 A 0.834139
AFFX-PheX-3_at 21.4 A 0.300606
AFFX-ThrX-5_at 1.6 A 0.672935
AFFX-ThrX-M_at 1.9 A 0.52976

Total number of rows: 45101

Table truncated, full table size 1198 Kbytes.




Supplementary file Size Download File type/resource
GSM29716.CEL.gz 6.3 Mb (ftp)(http) CEL
GSM29716.EXP.gz 267 b (ftp)(http) EXP
GSM29716.RPT.gz 1.1 Kb (ftp)(http) RPT
GSM29716.txt.gz 2.4 Mb (ftp)(http) TXT
Raw data provided as supplementary file

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