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Sample GSM1008877 Query DataSets for GSM1008877
Status Public on Sep 03, 2013
Title Strain_HER2.rt.PIK3_plus_Dox_387_Arteaga
Sample type RNA
 
Channel 1
Source name Whole Mouse Reference RNA
Organism Mus musculus
Characteristics reference: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups
Biomaterial provider Charles Perou - UNC
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen RNeasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
Channel 2
Source name FVB_HER2.rt.PIK3_plus_Dox_387_tumor
Organism Mus musculus
Characteristics tumor: HER2 and PI3K H1047R overexpressing FVB mammary tumor
Biomaterial provider Carlos Arteaga - Vanderbilt University School of Medicine
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-125
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software
Description Mammary Tumor
Data processing Data for both channels were Lowess-normalized and then the log(2) ratio was taken
 
Submission date Sep 24, 2012
Last update date Jul 17, 2015
Contact name Charles M. Perou
E-mail(s) cperou@med.unc.edu
Organization name University of North Carolina at Chapel Hill
Department Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
Street address 12-044 Lineberger Comprehensive Cancer Center CB# 7295
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7264
Country USA
 
Platform ID GPL11383
Series (1)
GSE41118 Mutant PI3K cooperates with HER2 to promote mammary tumor formation and induces trastuzumab resistance in vivo

Data table header descriptions
ID_REF Spot Reference ID
VALUE log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN)
SPOT spot number on array
CH1_MEAN
CH1_SD standard deviation of channel 1 intensity
CH1_BKD_MEDIAN channel 1 background median intensity
CH1_BKD_SD standard deviation of channel 1 background median intensity
CH2_MEAN channel 2 mean intensity
CH2_SD standard deviation of channel 2 intensity
CH2_BKD_MEDIAN channel 2 background median intensity
CH2_BKD_SD standard deviation of channel 2 background median intensity
TOT_BPIX number of background pixels
TOT_SPIX number of spot pixels
CH2BN_MEDIAN channel 2 normalized background median intensity
CH2IN_MEAN channel 2 normalized mean intensity
CH1DL_MEAN channel 1 Lowess_normalized mean intensity
CH2DL_MEAN channel 2 Lowess_normalized mean intensity
LOG_RAT2N_MEAN log2_ratio of channel 2 normalized over channel 1 (global normalization)
CORR correlation coefficient among pixels
FLAG Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots

Data table
ID_REF VALUE SPOT CH1_MEAN CH1_SD CH1_BKD_MEDIAN CH1_BKD_SD CH2_MEAN CH2_SD CH2_BKD_MEDIAN CH2_BKD_SD TOT_BPIX TOT_SPIX CH2BN_MEDIAN CH2IN_MEAN CH1DL_MEAN CH2DL_MEAN LOG_RAT2N_MEAN CORR FLAG
1 -.3 1 12405 809 14 5 9840 985 42 15 10704 78 45 10580 12228 9930 -.234 .25 0
2 1.421 2 17 5 15 5 49 16 42 16 8640 88 45 52 2 7 1.222 -1 0
3 1.505 3 17 5 15 5 48 15 42 15 7280 84 45 51 2 6 1.585 .43 0
4 -.616 4 18 6 15 5 42 16 41 16 7354 94 44 45 2 1 -1 -1 0
5 .474 5 20 6 15 5 49 14 42 16 7238 82 45 52 5 7 .485 .27 0
6 -.076 6 21 7 15 5 48 17 42 16 7272 86 45 51 6 6 0 .38 0
7 .585 7 18 5 15 5 46 18 41 16 7308 88 44 49 3 5 .737 .42 0
8 .261 8 18 6 15 5 45 16 41 16 7330 88 44 48 3 4 .415 -1 0
9 1.046 9 17 7 15 5 45 16 42 16 7306 88 45 48 1 3 1.585 -1 0
10 -.41 10 19 7 15 5 44 16 42 16 7356 86 45 47 3 3 -1 .43 0
11 .747 11 17 6 15 5 45 18 42 16 7528 80 45 48 2 3 .585 -1 0
12 1.453 12 17 6 15 5 49 22 42 16 7414 84 45 52 2 7 1.807 -1 0
13 .779 13 18 7 15 5 48 15 43 16 7364 92 45 51 3 5 1 .04 0
14 1.278 14 17 5 15 5 48 18 43 17 7404 90 46 51 2 6 1.322 .47 0
15 2.353 15 16 6 15 5 52 19 43 17 7456 90 46 55 1 9 3.17 -1 0
16 -.902 16 24 10 15 5 48 16 44 17 7300 82 47 51 9 4 -1.171 .32 0
17 -.532 17 19 5 15 5 45 19 43 17 7288 84 46 48 3 2 -1 -1 0
18 .995 18 20 8 15 5 53 17 43 17 7260 84 46 56 5 10 1 -1 0
19 -.802 19 19 8 15 5 44 14 43 17 7332 88 46 47 3 2 -2 .28 0
20 1.366 20 19 6 15 5 55 21 43 17 7360 84 46 59 4 12 1.7 .42 0

Total number of rows: 180880

Table truncated, full table size 12651 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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