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Sample GSM308553 Query DataSets for GSM308553
Status Public on Jan 01, 2009
Title DF 2 h (Cy3) vs. 0 h (Cy5)
Sample type RNA
 
Channel 1
Source name Dermal fibroblasts, IL-1-treated (2 h)
Organism Mus musculus
Characteristics Strain: C57BL/6
Treatment protocol Cells were incubated with 20 ng/ml IL-1 for 0, 1, 2, or 4 h.
Growth protocol Mouse dermal fibroblasts were cultured in DMEM medium containing antibiotics and 10% FBS.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions.
Label Cy3
Label protocol Fluorescent cRNA was generated from 5 µg of total RNA using Agilent Two-Color Quick Amp Labeling Kit. The reaction and purification conditions were based on the manufacturer's protocol.
 
Channel 2
Source name Dermal fibroblasts, untreated (0 h)
Organism Mus musculus
Characteristics Strain: C57BL/6
Treatment protocol Cells were incubated with 20 ng/ml IL-1 for 0, 1, 2, or 4 h.
Growth protocol Mouse dermal fibroblasts were cultured in DMEM medium containing antibiotics and 10% FBS.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions.
Label Cy5
Label protocol Fluorescent cRNA was generated from 5 µg of total RNA using Agilent Two-Color Quick Amp Labeling Kit. The reaction and purification conditions were based on the manufacturer's protocol.
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially with GE Wash Buffer 1 at room temperature and GE Wash Buffer 2 at 31°C.
Scan protocol Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5).
Description Replicate 2 of 2
Data processing LOWESS normalized, background-subtracted data obtained from log2 of processed test signal/processed reference signal. Agilent software was used.
 
Submission date Jul 29, 2008
Last update date Jul 30, 2008
Contact name Jin Mo Park
E-mail(s) jmpark@cbrc2.mgh.harvard.edu
Phone 617-643-2328
Organization name Massachusetts General Hospital
Department Cutaneous Biology Research Center
Street address 149 Thirteenth Street
City Charlestown
State/province MA
ZIP/Postal code 02129
Country USA
 
Platform ID GPL2872
Series (1)
GSE12285 Interleukin-1-induced gene expression in mouse dermal fibroblasts

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio representing test/reference (Ch1/Ch2)

Data table
ID_REF VALUE
1 -8.805043329
2 -1.599917485
3 -0.270655083
4 -0.435247875
5 -0.100972108
6 -1.470502439
7 -8.340225277
8 0.211723719
9 -0.873367145
10 -0.093364518
11 -0.847217212
12 -0.925243518
13 -1.015045617
14 -9.077763408
15 -0.542093143
16 -1.382055446
17 0.084763604
18 -0.753838617
19 -1.347977193
20 -0.051042592

Total number of rows: 43790

Table truncated, full table size 773 Kbytes.




Supplementary file Size Download File type/resource
GSM308553.txt.gz 11.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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