NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM262242 Query DataSets for GSM262242
Status Public on Mar 30, 2009
Title 4164N.normal.Cy3
Sample type RNA
 
Channel 1
Source name Normal epithelial tissue from murine mammary glands
Organism Mus musculus
Characteristics Sample identifier: 4164N; Diagnosis: normal; Sex: Female; Strain: FVB/N
Extracted molecule total RNA
Extraction protocol Phenol-chloroform extraction
Label Cy3
Label protocol 4ng of extracted RNA was subjected to two rounds of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy3-labeled cRNA was prepared from 4-5ug total RNA using Ambion's MessageAmp kit.
 
Channel 2
Source name Stratagene universal mouse reference
Organism Mus musculus
Characteristics None
Biomaterial provider Stratagene
Extracted molecule total RNA
Extraction protocol No extraction
Label Cy5
Label protocol 4ng of extracted RNA was subjected to one round of linear T7 RNA amplification (Amino Allyl MessageAmp kit, Ambion) according to manufacturer's protocol. Cy5-labeled cRNA was prepared from 4-5 ug total RNA using Ambion's MessageAmp kit.
 
 
Hybridization protocol Following fragmentation, 750ng of cRNA was hybridized to Agilent's Whole Mouse Genome expression array (G4122A) according to the protocols provided by the manufacturer.
Scan protocol Array was scanned using Agilent's dual-laser microarray scanner (Model G2505B), and Cy5/Cy3-signals were quantified using Agilent's Feature Extraction software (Palo Alto, CA).
Description RNA isolated from laser capture microdissected mammary tissue.
Data processing Raw Cy5 and Cy3 intensities were background corrected using the RMA background correction algorithm. Data was transformed to log2 ratios and within array normalization was performed using spatial and intensity-dependent loess.
 
Submission date Feb 04, 2008
Last update date Mar 30, 2009
Contact name Robert Lesurf
Organization name Washington University in St. Louis
Department McDonnell Genome Institute
Lab Griffith Lab
Street address 4444 Forest Park Ave
City St. Louis
State/province MO
ZIP/Postal code 63112
Country USA
 
Platform ID GPL2872
Series (1)
GSE10450 Met induces mammary tumors with diverse histologies and is associated with poor outcome and human basal breast cancer

Data table header descriptions
ID_REF
VALUE -[INV_VALUE]
gMeanSignal The mean foreground signal in the Cy3 channel
gMedianSignal The median foreground signal in the Cy3 channel
gBGMeanSignal The mean background signal in the Cy3 channel
gBGMedianSignal The median background signal in the Cy3 channel
rMeanSignal The mean foreground signal in the Cy5 channel
rMedianSignal The median foreground signal in the Cy5 channel
rBGMeanSignal The mean background signal in the Cy5 channel
rBGMedianSignal The median background signal in the Cy5 channel
INV_VALUE log2 ratio of normalized Cy5 to Cy3 signal

Data table
ID_REF VALUE gMeanSignal gMedianSignal gBGMeanSignal gBGMedianSignal rMeanSignal rMedianSignal rBGMeanSignal rBGMedianSignal INV_VALUE
1 1.97672 1732.143 1740 44.99054 45 611.6786 626.5 44.12934 44 -1.97672069098001
2 -0.0338531 88.33333 88.5 45.09023 45 50.83333 50 43.7782 44 0.0338530737190368
3 -0.341438 1007.063 1031 46.01075 46 1399.063 1403 44.15412 44 0.341438484403799
4 -0.761378 103.88 101 45.49627 45.5 166.36 164 43.8097 43.5 0.761378412400488
5 -0.0356104 793.3 807.5 46.50526 46 919.5667 909.5 43.81754 44 0.0356104482585771
6 1.76296 369.4667 378.5 46.10545 46 154.8667 154.5 43.75636 44 -1.76296069276554
7 3.56087 896.2692 883.5 45.86397 46 148.5 147.5 43.93015 44 -3.56087263265205
8 -0.472313 365.931 358 45.95941 45 471.5862 465 43.95203 44 0.472313229269983
9 1.12276 299.3214 302 46.47388 46 170.2143 171 43.8209 44 -1.12275519720335
10 0.915926 4879.844 4723.5 45.97531 46 2836.938 2780 43.73251 44 -0.915926179439555
11 -0.23392 126.5172 124 46.45221 46 129.7586 130 43.48162 43 0.233920260100465
12 0.774775 219.8214 223 46.27899 46 123.2143 122.5 43.65217 44 -0.774775399394969
13 0.693902 272.931 269 46.09964 46 193.3448 191 43.46975 44 -0.693901959356458
14 3.60768 972.8929 959.5 47.10219 47 164.3929 164 43.74088 44 -3.60767792446066
15 0.247598 155.3103 161 46.72161 46 105.2414 105 43.39927 43 -0.247597853681610
16 0.255941 261.8 256 46.5539 46 231.4333 235 43.46097 44 -0.255940809313374
17 -2.54856 374.2759 368 47.64312 48 1678.207 1646 43.92565 44 2.54856032765948
18 1.72532 2075.931 2046 46.64504 46 842.1034 846 44.04198 44 -1.72531953840602
19 -0.0481411 98 97 46.50929 46 74.8 73 43.99628 44 0.0481410595499661
20 -0.806158 4975.276 4945 47.47727 47 8931.862 8880 44.23864 44 0.806157504149649

Total number of rows: 43790

Table truncated, full table size 3572 Kbytes.




Supplementary file Size Download File type/resource
GSM262242.txt.gz 11.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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