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Sample GSM80447 Query DataSets for GSM80447
Status Public on May 01, 2007
Title C57Bl6_MMTV_Cre_BRCA1CoCo_p53het_113a_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_113a
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_113a_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 -.453 22575 117 45 40 9 114 80 57 35 858 156 62 125 77 56 -.29 .47 0 Y -.453
2 .001 22470 56 13 41 8 78 41 59 38 730 156 64 85 16 16 .485 .1 0 Y .001
3 .322 22365 95 31 41 8 130 68 61 39 754 156 67 142 54 68 .474 .4 0 N .322
4 .343 22260 62 17 41 8 93 52 60 36 754 156 65 102 23 29 .817 .31 0 N .343
5 -1.279 22155 1963 1000 40 9 800 399 58 37 730 156 63 879 1860 766 -1.238 .93 0 N -1.279
6 -2.405 22050 273 146 40 10 100 60 57 36 730 156 62 109 230 43 -2.308 .35 0 N -2.405
7 -1.585 21945 112 44 40 10 84 52 58 35 730 156 63 92 74 24 -1.311 .18 0 Y -1.585
8 -1.147 21840 137 49 41 9 102 56 58 34 730 156 63 112 96 43 -.971 .4 0 N -1.147
9 .289 21735 57 14 41 9 86 45 61 36 754 156 67 94 18 22 .755 .13 0 N .289
10 .782 21630 76 26 41 9 120 67 56 34 754 156 61 131 36 62 1 .47 0 N .782
11 .337 21525 103 35 41 8 138 83 59 37 730 156 64 151 62 78 .489 .56 0 N .337
12 .287 21420 77 24 41 8 109 57 61 36 730 156 67 119 37 45 .53 .38 0 N .287
13 .899 21315 143 52 40 8 242 143 60 36 730 156 65 265 100 186 .958 .77 0 N .899
14 -1.751 21210 118 40 40 8 82 39 57 37 730 156 62 90 81 24 -1.478 .18 0 Y -1.751
15 -.114 21105 300 144 41 8 271 151 56 38 754 156 61 297 245 226 -.134 .84 0 N -.114
16 .598 21000 63 17 41 9 97 54 57 35 754 156 62 106 24 36 1 .27 0 N .598
17 .573 20895 144 58 40 8 204 125 56 34 730 156 61 224 101 151 .648 .75 0 N .573
18 -.788 20790 1081 501 40 9 603 276 57 34 730 156 62 662 990 573 -.796 .93 0 N -.788
19 -.41 20685 3733 2260 41 9 2858 1694 56 35 730 156 61 3140 3706 2790 -.262 .95 0 N -.41
20 .119 20580 335 144 41 9 342 177 59 36 730 156 64 375 276 300 .081 .88 0 N .119

Total number of rows: 22575

Table truncated, full table size 1822 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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