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Sample GSM80430 Query DataSets for GSM80430
Status Public on May 01, 2007
Title C57Bl6_MMTV_Cre_BRCA1CoCo_p53het_108b_FURTH
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 C57Bl6_MMTV_Cre_BRCA1CoCo_p53het_108b
Organism Mus musculus
Characteristics mammary tumor
Biomaterial provider Priscilla Furth - 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 C57Bl6_MMTV_Cre_BRCA1CoCo_p53het_108b_FURTH
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Oct 27, 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 -1.936 22575 184 83 49 15 84 47 51 26 858 156 43 72 130 34 -2.218 .39 0 Y -1.936
2 .1 22470 75 24 48 14 64 32 51 27 730 156 43 55 18 19 -1.171 .07 0 Y .1
3 .016 22365 147 58 49 28 158 83 52 29 754 156 44 136 101 102 -.091 .72 0 N .016
4 .266 22260 97 32 49 28 99 50 52 28 754 156 44 85 43 52 -.228 .3 0 N .266
5 -.458 22155 6018 3390 49 14 7820 4651 51 27 730 156 43 6741 7982 5809 .166 .94 0 N -.458
6 -3.526 22050 890 435 50 14 146 75 50 26 730 156 43 125 963 83 -3.351 .74 0 N -3.526
7 -1.958 21945 180 85 49 14 82 41 51 29 730 156 43 70 125 32 -2.279 .33 0 Y -1.958
8 -1.832 21840 358 184 48 13 159 79 52 29 730 156 44 137 343 96 -1.737 .78 0 N -1.832
9 .04 21735 84 26 49 13 71 41 50 28 754 156 43 61 26 27 -.96 .23 0 N .04
10 .044 21630 135 56 49 13 142 73 51 27 754 156 43 122 87 89 -.122 .68 0 N .044
11 -.331 21525 230 118 50 13 226 129 51 27 730 156 43 194 199 158 -.253 .82 0 N -.331
12 .492 21420 141 58 49 13 194 101 51 28 730 156 43 167 96 136 .431 .71 0 N .492
13 .154 21315 217 98 49 13 286 148 53 28 730 156 45 246 187 208 .258 .83 0 N .154
14 -1.919 21210 190 88 48 14 88 44 52 29 730 156 44 75 139 36 -2.198 .41 0 Y -1.919
15 1.268 21105 1411 768 49 14 5445 3303 51 27 754 156 43 4693 1746 4206 1.771 .95 0 N 1.268
16 .48 21000 91 31 49 13 98 55 52 26 754 156 44 84 37 51 -.071 .39 0 N .48
17 -.131 20895 218 112 49 13 242 140 53 27 730 156 45 208 186 170 -.053 .86 0 N -.131
18 -.65 20790 4082 2245 51 13 4460 2710 55 29 698 156 47 3844 5278 3363 -.086 .94 0 N -.65
19 -.464 20685 11114 6533 50 14 14630 9380 52 27 698 156 44 12612 14914 10814 .184 .91 0 N -.464
20 -.625 20580 612 283 49 77 566 271 50 28 698 156 43 487 669 433 -.342 .87 0 N -.625

Total number of rows: 22575

Table truncated, full table size 1906 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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