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Sample GSM1046469 Query DataSets for GSM1046469
Status Public on Nov 04, 2013
Title C57Bl6_Mammary_Norm_437_1_FURTH
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 C57Bl6_Mammary_Norm_437_1_FURTH
Organism Mus musculus
Characteristics sample: Normal Mammary
Biomaterial provider Priscilla Furth - Georgetown University
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 Normal Mammary
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 GPL10732
Series (1)
GSE42640 Transcriptomic Classification of Genetically Engineered Mouse Models of Breast Carcinoma Identifies Human Subtype Counterparts

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 -.156 22575 185 58 108 33 95 58 58 38 521 156 46 76 56 50 -1.358 .26 0
2 -.422 22470 182 58 110 35 83 48 59 36 544 156 47 66 48 35 -1.921 .2 0
3 .334 22365 188 61 109 34 126 71 60 36 568 156 48 101 64 81 -.576 .44 0
4 -.019 22260 177 56 107 33 93 54 58 40 568 156 46 75 49 49 -1.272 .16 0
5 .85 22155 2162 1181 106 33 6284 3655 56 37 544 156 45 5067 2665 4804 1.289 .98 0
6 -2.991 22050 541 279 104 31 112 60 57 36 544 156 45 90 437 54 -3.279 .46 0
7 -.129 21945 178 53 106 32 90 50 57 37 544 156 45 72 50 46 -1.415 .18 0
8 -1.011 21840 368 149 110 34 194 110 56 38 544 156 45 156 267 132 -1.218 .72 0
9 -.348 21735 185 58 108 34 87 49 57 39 568 156 45 70 54 42 -1.621 .25 0
10 .027 21630 197 71 105 33 121 69 56 38 568 156 45 97 76 78 -.824 .35 0
11 -.687 21525 311 110 105 32 188 109 57 38 544 156 45 151 208 129 -.957 .67 0
12 -.141 21420 223 80 106 31 144 93 58 38 544 156 46 116 105 95 -.742 .51 0
13 .962 21315 236 80 107 31 329 197 59 40 544 156 47 265 133 260 .757 .73 0
14 -.184 21210 179 51 106 32 89 51 57 39 544 156 45 71 51 45 -1.49 .14 0
15 -1.64 21105 437 204 104 32 173 111 56 40 568 156 45 139 348 111 -1.826 .69 0
16 -.281 21000 184 60 103 29 94 57 58 38 568 156 46 75 59 48 -1.482 .21 0
17 .036 20895 232 80 103 31 180 100 60 34 544 156 48 145 122 125 -.411 .64 0
18 -.673 20790 1410 799 103 34 1243 747 58 35 544 156 46 1002 1571 985 -.452 .98 0
19 .665 20685 5484 3050 107 34 16308 9317 59 38 544 156 47 13151 7422 11770 1.285 1 0
20 .443 20580 369 153 109 33 494 278 57 38 544 156 45 398 289 393 .441 .87 0

Total number of rows: 22575

Table truncated, full table size 1780 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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