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Sample GSM69606 Query DataSets for GSM69606
Status Public on May 01, 2007
Title FVB_DMBA_6_Squa_GLAZER
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_DMBA_6_Squa
Organism Mus musculus
Characteristics mammary tumor
Biomaterial provider Robert Glazer - Georgetown
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_DMBA_6_Squa_GLAZER
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 -1.834 22575 78 31 34 5 50 18 37 11 521 156 33 44 45 12 -2 .45 0 Y -1.834
2 .59 22470 40 8 34 5 43 12 37 11 544 156 33 38 4 7 -.264 .03 0 Y .59
3 .118 22365 80 29 34 5 95 45 38 10 568 156 33 84 49 53 .149 .8 0 N .118
4 .076 22260 55 14 34 5 60 23 37 11 568 156 33 53 21 22 -.071 .56 0 N .076
5 -.683 22155 567 328 34 5 409 261 37 10 544 156 33 365 564 351 -.683 .95 0 N -.683
6 -2.539 22050 176 75 34 5 66 27 38 11 544 156 33 58 151 26 -2.506 .69 0 N -2.539
7 -1.995 21945 86 31 34 5 51 19 37 11 544 156 33 45 53 13 -2.114 .42 0 Y -1.995
8 -1.407 21840 91 32 34 5 60 22 36 11 544 156 32 53 60 22 -1.442 .6 0 N -1.407
9 .015 21735 44 9 34 5 46 15 38 11 568 156 33 41 8 8 -.322 .22 0 N .015
10 .085 21630 64 20 34 5 73 32 38 11 568 156 33 65 31 33 .094 .71 0 N .085
11 -.331 21525 88 34 34 6 87 40 38 11 544 156 33 77 57 45 -.295 .78 0 N -.331
12 -.178 21420 66 21 34 6 68 27 37 11 544 156 33 60 33 29 -.245 .66 0 N -.178
13 .129 21315 125 44 34 5 150 70 36 12 544 156 32 133 97 106 .151 .89 0 N .129
14 -1.989 21210 89 34 34 5 52 17 37 11 544 156 33 46 57 14 -2.083 .47 0 Y -1.989
15 .945 21105 165 70 34 5 320 179 37 10 568 156 33 285 138 267 .944 .93 0 N .945
16 .671 21000 54 14 34 5 72 28 38 11 568 156 33 64 20 32 .632 .66 0 N .671
17 .24 20895 131 58 34 5 168 90 37 11 544 156 33 149 103 122 .258 .92 0 N .24
18 -.594 20790 488 267 34 5 374 231 38 10 544 156 33 333 479 317 -.597 .94 0 N -.594
19 -.439 20685 1403 869 35 5 1238 827 37 11 544 156 33 1105 1492 1100 -.351 .96 0 N -.439
20 -.19 20580 243 114 34 5 242 126 37 10 544 156 33 216 221 193 -.191 .95 0 N -.19

Total number of rows: 22575

Table truncated, full table size 1789 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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