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Sample GSM1046723 Query DataSets for GSM1046723
Status Public on Nov 04, 2013
Title FVB_MMTV_PyMT_103572-1_untreated_GMurrow
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_MMTV_PyMT_103572-1_untreated_GMurrow
Organism Mus musculus
Characteristics sample: MMTV PyMT
Biomaterial provider Charles Perou - UNC
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 Nov 29, 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 GPL2881
Series (2)
GSE42640 Transcriptomic Classification of Genetically Engineered Mouse Models of Breast Carcinoma Identifies Human Subtype Counterparts
GSE65677 The Six1 oncoprotein represses translation of p53 via concomitant regulation of RPL26 and microRNA-27a

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 .454 22575 92 22 53 18 102 51 51 36 377 52 35 71 38 52 -.116 .14 0
2 -2.946 22470 85 22 59 18 64 45 61 35 233 32 42 44 24 3 -3.699 .04 0
3 .621 22365 99 23 52 35 127 59 50 39 587 80 34 88 48 74 .2 .6 0
4 -.425 22260 83 18 51 14 66 33 50 29 496 80 34 46 26 19 -1.415 .17 0
5 -.747 22155 948 214 52 18 1047 357 50 31 665 120 34 732 1224 729 -.36 .95 0
6 -2.973 22050 303 73 53 35 91 55 51 38 666 120 35 63 280 35 -3.158 .35 0
7 3.184 21945 56 13 54 54 72 38 52 63 499 80 36 50 2 19 2.807 .03 0
8 -1.517 21840 344 61 54 19 203 83 49 35 598 80 34 141 357 124 -1.438 .75 0
9 -.243 21735 84 26 53 23 67 40 49 39 512 80 34 46 25 21 -1.37 .08 0
10 .206 21630 101 23 53 23 104 61 48 37 504 80 33 72 48 55 -.3 .43 0
11 .7 21525 145 34 52 18 258 109 50 31 686 120 34 180 109 177 .651 .75 0
12 .456 21420 108 26 52 13 136 71 50 30 576 80 34 95 59 81 .123 .49 0
13 .02 21315 127 33 52 14 140 71 50 35 700 120 34 97 81 82 -.252 .52 0
14 -.198 21210 94 23 52 13 84 56 52 33 326 52 36 58 39 34 -.932 .17 0
15 -.131 21105 278 59 52 13 380 160 50 30 682 120 34 265 285 261 .031 .85 0
16 -.078 21000 76 20 52 15 61 29 47 34 508 80 32 42 18 17 -1.262 .1 0
17 -.233 20895 140 32 52 14 141 78 50 34 701 120 34 98 97 82 -.46 .56 0
18 -.983 20790 1618 695 50 14 1595 664 53 36 638 120 37 1115 2185 1106 -.54 .94 0
19 -.071 20685 2157 598 54 15 4058 1301 48 36 704 120 33 2837 2976 2832 .415 .97 0
20 -.055 20580 161 43 52 14 188 96 48 32 700 120 33 131 125 121 -.154 .69 0

Total number of rows: 22575

Table truncated, full table size 1709 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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