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Sample GSM1008872 Query DataSets for GSM1008872
Status Public on Sep 03, 2013
Title Strain_HER2.rt.PIK3_plus_Dox_209_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_209_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 -.46 1 11807 1031 12 4 7248 1167 43 16 10624 74 78 13178 10813 7859 .152 -1 0
2 1.163 2 25 9 12 4 62 22 44 16 8692 82 80 112 10 24 1.415 .65 0
3 1.229 3 49 35 12 4 95 62 44 16 7390 82 80 172 28 67 1.354 .86 0
4 1.503 4 56 44 12 4 117 85 44 16 7370 88 80 212 33 95 1.618 .88 0
5 1.613 5 29 13 12 4 76 29 44 16 7558 82 80 138 13 41 1.858 .75 0
6 .809 6 26 12 12 4 58 20 43 16 7544 82 78 105 11 20 1.055 .46 0
7 -.52 7 18 5 12 4 45 18 43 16 7290 90 78 81 4 3 -1 -1 0
8 2.45 8 14 5 12 4 47 18 43 16 7314 86 78 85 1 7 2.807 .43 0
9 .864 9 17 5 12 4 48 20 43 16 7466 88 78 87 4 7 1.17 .27 0
10 2.096 10 14 5 12 4 49 17 43 16 7496 86 78 89 2 8 2.459 -1 0
11 -.086 11 16 6 12 4 44 14 43 16 7356 84 78 80 2 2 -1 -1 0
12 .842 12 17 4 12 4 48 16 43 15 7390 90 78 87 3 7 1.17 .3 0
13 .118 13 17 5 12 4 44 17 43 16 7494 84 78 80 2 3 -1 .35 0
14 .853 14 18 5 12 4 50 19 43 16 7484 86 78 90 5 9 1.263 .41 0
15 -.376 15 18 6 12 4 46 14 44 16 7386 92 80 83 4 3 -.737 .37 0
16 0 16 18 6 12 4 43 11 44 16 7370 82 80 78 0 0 0 -1 0
17 0 17 16 6 12 4 43 16 44 16 7538 94 80 78 0 0 0 .09 0
18 .495 18 16 4 12 4 46 16 44 16 7462 82 80 83 2 3 0 .18 0
19 .728 19 18 5 12 4 49 19 43 16 7392 88 78 89 5 8 1.138 .46 0
20 1.31 20 15 5 12 4 46 14 43 16 7350 86 78 83 2 5 .737 .32 0

Total number of rows: 180880

Table truncated, full table size 12629 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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