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Sample GSM69612 Query DataSets for GSM69612
Status Public on May 01, 2007
Title FVB_MMTV_Neu_8-2-99_GREEN
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_Neu_8-2-99
Organism Mus musculus
Characteristics mammary tumor
Biomaterial provider Jeffrey Green - NCI
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_Neu_8-2-99_GREEN
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 -4.571 22575 502 221 47 11 51 17 36 11 521 156 42 60 402 16 -4.644 .4 0 Y -4.571
2 .119 22470 58 15 47 11 39 11 36 11 544 156 42 45 5 5 -1.873 -1 0 Y .119
3 .825 22365 108 37 48 1859 116 49 36 286 568 156 42 136 52 92 .648 .77 0 N .825
4 .095 22260 76 52 48 2480 51 19 36 718 568 156 42 60 19 21 -.637 .82 0 N .095
5 -1.335 22155 1404 562 49 37 616 270 36 11 544 156 42 724 1408 558 -.991 .98 0 N -1.335
6 -3.146 22050 293 119 48 11 58 19 37 12 544 156 43 68 213 24 -3.293 .47 0 N -3.146
7 -4.891 21945 482 222 48 12 48 24 37 12 544 156 43 56 376 12 -5.059 .23 0 Y -4.891
8 -.879 21840 145 55 47 13 75 31 36 12 544 156 42 88 83 45 -1.092 .73 0 N -.879
9 .044 21735 63 15 48 13 41 14 36 12 568 156 42 48 8 8 -1.322 .03 0 N .044
10 .281 21630 91 28 47 11 70 27 36 12 568 156 42 82 35 42 -.138 .61 0 N .281
11 .572 21525 114 41 48 12 111 52 37 12 544 156 43 130 57 85 .398 .81 0 N .572
12 -.36 21420 86 25 48 12 54 22 38 12 544 156 44 63 27 21 -1 .41 0 N -.36
13 .393 21315 145 45 48 11 142 57 38 12 544 156 44 167 87 115 .343 .84 0 N .393
14 -5.023 21210 519 219 48 11 48 17 37 11 544 156 43 56 410 12 -5.158 .3 0 Y -5.023
15 -.068 21105 267 115 48 11 230 111 37 11 568 156 43 270 210 200 .052 .94 0 N -.068
16 -.063 21000 80 23 48 11 53 18 37 11 568 156 43 62 23 22 -.751 .35 0 N -.063
17 .857 20895 182 77 47 11 257 135 37 12 544 156 43 302 128 231 .94 .93 0 N .857
18 -1.131 20790 1039 596 47 12 519 317 37 12 544 156 43 610 1023 467 -.806 .97 0 N -1.131
19 -.494 20685 2787 1515 48 11 2217 1289 36 11 544 156 42 2608 2901 2059 -.094 .98 0 N -.494
20 -.122 20580 313 161 48 12 266 149 35 11 544 156 41 312 258 237 .033 .95 0 N -.122

Total number of rows: 22575

Table truncated, full table size 1846 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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