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Sample GSM69645 Query DataSets for GSM69645
Status Public on May 01, 2007
Title FVB_Wap_Myc_CA02_540A_CHURCHILL
Sample type RNA
 
Channel 1
Source name Mouse reference
Organism Mus musculus
Characteristics Whole mouse total RNA
Biomaterial provider Cam Patterson-UNC-CH
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name FVB_Wap_Myc_CA02_540A
Organism Mus musculus
Characteristics mammary tumor
Biomaterial provider Gary Churchill - JAX
Extracted molecule total RNA
Label Cy5
 
 
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software.
Description FVB_Wap_Myc_CA02_540A_CHURCHILL
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Aug 11, 2005
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 GPL891
Series (3)
GSE3165 Identification of conserved gene expression features across human and murine mammary tumors
GSE14457 Rb deletion in mammary stem/progenitor epithelium induces tumors with features of luminal-B or basal-like breast cancer
GSE65677 The Six1 oncoprotein represses translation of p53 via concomitant regulation of RPL26 and microRNA-27a
Relations
Affiliated with GSE34479

Data table header descriptions
ID_REF Spot Reference ID
VALUE same as UNF_VALUE but with flagged values removed
SPOT spot number on array
CH1_MEAN channel 1 mean intensity
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 (CH2IN_MEAN - CH2BN_MEDIAN) over (CH1_MEAN - CH1_BKD_MEDIAN), CH2IN_MEAN and CH2BN_MEDIAN are global-normalized intensities
CORR correlation coefficient among pixels
FLAG Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots
CONTROL Y: control gene; N: not control
UNF_VALUE LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN

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 CONTROL UNF_VALUE
1 -4.712 22575 594 296 44 9 59 23 41 14 550 156 43 62 509 19 -4.837 .45 0 Y -4.712
2 .145 22470 64 18 45 10 47 17 42 14 576 156 44 50 9 10 -1.662 .13 0 Y .145
3 .182 22365 94 31 45 18 74 32 41 24 600 156 43 78 37 42 -.486 .51 0 N .182
4 .387 22260 69 22 44 19 53 19 41 23 600 156 43 56 15 19 -.943 .23 0 N .387
5 -1.049 22155 1279 669 44 10 817 444 42 15 576 156 44 869 1407 680 -.582 .97 0 N -1.049
6 -3.813 22050 276 156 43 10 53 21 42 15 576 156 44 56 189 13 -4.265 .23 0 N -3.813
7 -5.295 21945 485 275 43 15 51 19 43 16 576 156 45 54 372 9 -5.644 .18 0 Y -5.295
8 -2.849 21840 156 85 43 16 49 16 41 15 600 156 43 52 80 11 -3.644 .22 0 N -2.849
9 .12 21735 68 19 43 11 50 19 41 14 600 156 43 53 14 15 -1.322 .18 0 N .12
10 .261 21630 81 28 43 10 64 25 41 15 576 156 43 68 27 32 -.604 .43 0 N .261
11 -.507 21525 144 59 42 9 96 45 40 14 576 156 42 102 90 63 -.766 .75 0 N -.507
12 -.214 21420 91 32 43 84 63 25 41 55 576 156 43 67 34 30 -1 .84 0 N -.214
13 .316 21315 108 39 44 84 98 47 41 55 576 156 43 104 54 67 -.069 .84 0 N .316
14 -4.701 21210 501 314 44 11 54 19 40 15 600 156 42 57 407 15 -4.921 .29 0 Y -4.701
15 -.695 21105 286 144 44 11 193 99 42 14 600 156 44 205 243 150 -.589 .92 0 N -.695
16 -.106 21000 69 21 44 10 49 18 42 15 576 156 44 52 13 12 -1.644 .25 0 N -.106
17 .162 20895 155 71 44 84 152 81 42 21 576 156 44 161 104 116 .076 .65 0 N .162
18 -2.29 20790 1020 809 44 24 274 200 41 16 576 156 43 291 1054 215 -1.977 .96 0 N -2.29
19 .086 20685 4034 2298 43 19 7400 4254 40 16 576 156 42 7872 5260 5583 .972 .99 0 N .086
20 -.417 20580 224 136 44 14 171 106 41 14 600 156 43 181 176 132 -.383 .9 0 N -.417

Total number of rows: 22575

Table truncated, full table size 1858 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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