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Sample GSM262667 Query DataSets for GSM262667
Status Public on Mar 30, 2009
Title 567T.tumor.Cy5.45k
Sample type RNA
 
Channel 1
Source name Stratagene universal mouse reference
Organism Mus musculus
Characteristics None
Biomaterial provider Stratagene
Extracted molecule total RNA
Extraction protocol No extraction
Label Cy3
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. Cy3-labeled cRNA was prepared from 4-5 ug total RNA using Ambion's MessageAmp kit.
 
Channel 2
Source name Tumor epithelial tissue from murine mammary glands
Organism Mus musculus
Characteristics Sample identifier: 567T; Diagnosis: adenocarcinoma with sclerosis; Sex: Female; Strain: FVB/N
Extracted molecule total RNA
Extraction protocol Phenol-chloroform extraction
Label Cy5
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. Cy5-labeled cRNA was prepared from 4-5ug total RNA using Ambion's MessageAmp kit.
 
 
Hybridization protocol Following fragmentation, 825ng of cRNA was hybridized to Agilent's Whole Mouse Genome expression array (G4122F) 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 05, 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 GPL4134
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 log2 ratio of normalized Cy5 to Cy3 signal
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

Data table
ID_REF VALUE gMeanSignal gMedianSignal gBGMeanSignal gBGMedianSignal rMeanSignal rMedianSignal rBGMeanSignal rBGMedianSignal
1 0.488418396776527 15339.59 15104 38.33125 37 25092.55 24921.5 44.31875 43
2 0.00350900953293731 47.69697 47.5 38.74327 38 51.81818 50.5 43.10559 42
3 0.0262566034320315 46.98413 47 38.77354 37.5 52.61905 52 44.09865 44
4 -0.0637362365138365 49.78125 48 38.36383 37 49.67188 49 42.7451 42
5 -0.0784711204977455 48.64407 50 38.27314 38 47.79661 46 43.73138 43
6 -0.0618289822835472 49.47541 48 37.49561 37 49.59016 48 43.37939 42
7 0.0069819116055303 44.30159 46 38 37 49.26984 49 42.48807 42
8 -0.0445328980375947 48.87302 49 38.9016 38 50.15873 50 44.15561 43
9 -0.0287646932809391 48.65 47 38.70536 38 50.93333 51 42.93304 42
10 -0.0631034573676246 45.45763 46 38.00425 37 46 47 42.25053 41
11 0.089214822415471 41.96825 41 38.84211 38 52.30159 52 43.73474 44
12 1.28739470777121 55.69643 56.5 38.77282 38 122.2321 119.5 44.97452 45
13 1.18393225589146 292.4688 291 37.64842 37 337.5 331.5 42.58526 42
14 0.825035381034947 66.36508 62 37.91503 37 106.6984 105 42.22222 41
15 0.61500688532453 331.0625 319.5 38.95768 38 281.5938 273.5 42.65924 42
16 0.330874203379768 3403.309 3329 37.64859 37 2640.191 2554 43.22777 42
18 0.159242339651838 52.47458 52 38.80952 37 64.88136 64 43.18398 42
19 0.0920917229039553 76.08197 77 37.49087 37 78.2459 78 42.74442 42
20 -0.0709035920358687 56.09677 56 38.2376 37 54.74194 54.5 42.46074 42
21 -1.17172675653723 244.1525 238 38.99371 38 111.2542 111 42.00629 41

Total number of rows: 45018

Table truncated, full table size 3248 Kbytes.




Supplementary file Size Download File type/resource
GSM262667.txt.gz 13.1 Mb (ftp)(http) TXT
Processed data included within Sample table
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