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Sample GSM69625 Query DataSets for GSM69625
Status Public on May 01, 2007
Title FVB_MMTV_Wnt1_CA02_493A_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_MMTV_Wnt1_CA02_493A
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_MMTV_Wnt1_CA02_493A_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 -4.744 22575 1190 488 95 30 103 52 68 41 521 156 59 89 1013 37 -5.211 .33 0 Y -4.744
2 .536 22470 154 51 95 39 91 52 68 41 544 156 59 79 30 44 -1.561 .03 0 Y .536
3 -.165 22365 281 91 96 37 194 90 68 42 568 156 59 168 161 144 -.764 .63 0 N -.165
4 .212 22260 176 55 96 28 103 60 68 41 568 156 59 89 49 56 -1.415 .18 0 N .212
5 -1.72 22155 2379 1083 97 29 1281 681 66 41 544 156 57 1113 3022 917 -1.111 .93 0 N -1.72
6 -3.241 22050 703 259 95 29 116 62 63 41 544 156 54 100 551 58 -3.718 .42 0 N -3.241
7 -4.316 21945 1142 496 92 30 113 61 65 42 544 156 56 98 1001 50 -4.644 .37 0 Y -4.316
8 -1.669 21840 718 275 92 28 291 133 68 42 544 156 59 253 666 209 -1.69 .85 0 N -1.669
9 .36 21735 159 50 94 28 92 51 68 43 568 156 59 80 34 44 -1.63 .13 0 N .36
10 .412 21630 185 63 95 29 125 63 67 45 568 156 58 108 62 83 -.847 .33 0 N .412
11 .123 21525 245 93 94 30 186 93 69 44 544 156 60 161 127 138 -.58 .44 0 N .123
12 .055 21420 212 67 96 30 139 69 72 42 544 156 62 120 86 89 -1 .42 0 N .055
13 .048 21315 248 88 97 28 178 101 69 41 544 156 60 154 126 130 -.683 .39 0 N .048
14 -4.753 21210 1177 476 97 81 99 51 65 40 562 156 56 86 994 36 -5.158 .29 0 Y -4.753
15 1.014 21105 361 142 97 82 691 325 67 42 568 156 58 600 285 576 1.038 .86 0 N 1.014
16 -.217 21000 191 59 96 467 101 56 69 66 550 156 60 87 59 51 -1.816 .24 0 N -.217
17 -.013 20895 334 128 95 469 283 154 66 67 544 156 57 246 228 226 -.338 .17 0 N -.013
18 -.146 20790 2184 982 96 29 3756 1706 66 41 544 156 57 3266 2919 2638 .62 .96 0 N -.146
19 -.5 20685 5400 2329 98 29 8875 4164 67 40 544 156 58 7717 8127 5745 .531 .96 0 N -.5
20 -.603 20580 664 258 96 29 545 261 65 39 568 156 56 473 643 423 -.446 .9 0 N -.603

Total number of rows: 22575

Table truncated, full table size 1927 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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