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Sample GSM1046928 Query DataSets for GSM1046928
Status Public on Nov 04, 2013
Title FVB_NJ_NORMAL_CA03_603A_lactating
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_NJ_NORMAL_CA03_603A_lactating
Organism Mus musculus
Characteristics sample: Mammary Normal Lactating
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 Normal Lactating
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 -1.712 22575 60 19 30 4 48 16 38 13 521 156 33 42 31 9 -1.737 .21 0
2 .54 22470 34 5 30 4 45 18 39 14 544 156 34 40 4 5 .585 .08 0
3 1.951 22365 50 12 30 4 121 58 40 14 568 156 35 108 20 79 1.868 .8 0
4 .241 22260 38 7 30 4 49 19 38 14 568 156 33 43 8 10 .322 .14 0
5 -1.376 22155 577 322 30 4 262 156 37 14 544 156 33 233 565 217 -1.45 .95 0
6 -2.135 22050 123 53 30 4 61 23 39 13 544 156 34 54 94 21 -2.218 .52 0
7 -1.712 21945 60 18 30 3 48 15 38 13 544 156 33 42 31 9 -1.737 .2 0
8 -2.013 21840 83 33 30 3 52 20 38 13 544 156 33 46 54 13 -2.029 .36 0
9 -.361 21735 37 6 30 4 45 18 39 13 568 156 34 40 7 5 -.223 .09 0
10 .122 21630 46 10 30 3 58 25 39 13 568 156 34 51 16 18 .087 .46 0
11 -.257 21525 58 17 30 4 63 26 38 14 544 156 33 56 28 24 -.285 .54 0
12 -.043 21420 47 11 30 4 56 19 38 15 544 156 33 49 17 17 -.088 .36 0
13 1.69 21315 71 19 30 4 171 78 38 13 544 156 33 152 41 132 1.537 .87 0
14 -1.144 21210 63 20 30 4 54 51 38 12 544 156 33 48 34 15 -1.136 .44 0
15 -.407 21105 113 47 30 4 101 49 38 12 568 156 33 90 83 62 -.542 .84 0
16 .069 21000 39 7 30 4 49 18 38 14 568 156 33 43 9 10 .152 .21 0
17 5.877 20895 83 32 30 4 3415 2161 38 15 544 156 33 3049 55 3243 5.831 .95 0
18 -.915 20790 375 215 30 4 227 133 37 12 544 156 33 202 351 186 -1.029 .94 0
19 -.608 20685 1045 625 30 4 790 507 37 14 544 156 33 705 1079 708 -.595 .97 0
20 .568 20580 136 58 31 4 191 107 37 14 544 156 33 170 104 154 .384 .9 0

Total number of rows: 22575

Table truncated, full table size 1598 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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