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Sample GSM69599 Query DataSets for GSM69599
Status Public on May 01, 2007
Title FVB_DMBA_12_Spindle_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_12_Spindle
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_12_Spindle_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 -2.069 22575 79 28 35 5 46 17 38 14 521 156 40 49 38 9 -2.286 .18 0 Y -2.069
2 .541 22470 41 8 35 5 44 16 38 14 544 156 40 47 4 7 .223 .08 0 Y .541
3 .376 22365 59 16 34 5 63 23 38 13 568 156 40 67 21 28 .111 .51 0 N .376
4 .373 22260 46 9 34 5 50 19 38 13 568 156 40 53 10 13 .115 .2 0 N .373
5 -.526 22155 502 273 34 5 368 277 37 13 544 156 39 395 472 327 -.394 .88 0 N -.526
6 -2.238 22050 130 59 35 5 53 20 37 13 544 156 39 56 84 17 -2.482 .39 0 N -2.238
7 -1.815 21945 81 28 35 5 49 17 39 14 544 156 41 52 40 11 -2.065 .22 0 Y -1.815
8 -1.206 21840 76 28 34 5 53 23 39 13 544 156 41 56 36 15 -1.486 .29 0 N -1.206
9 .415 21735 42 8 34 5 46 16 38 13 568 156 40 49 6 9 .17 .14 0 N .415
10 -.194 21630 58 15 34 5 54 21 38 13 568 156 40 58 20 18 -.415 .35 0 N -.194
11 -.631 21525 73 23 35 5 58 22 39 14 544 156 41 62 33 21 -.855 .45 0 N -.631
12 .177 21420 57 15 35 5 59 23 40 14 544 156 43 63 19 21 -.138 .38 0 N .177
13 .222 21315 80 24 34 5 82 38 39 14 544 156 41 88 41 48 .031 .64 0 N .222
14 -1.908 21210 83 29 34 5 48 19 38 13 544 156 40 51 42 11 -2.158 .18 0 Y -1.908
15 2.171 21105 150 70 35 5 522 407 38 13 568 156 40 561 111 500 2.18 .83 0 N 2.171
16 .682 21000 48 10 35 5 53 20 37 13 568 156 39 56 11 18 .387 .33 0 N .682
17 .314 20895 81 28 34 5 85 41 38 13 544 156 40 91 42 52 .118 .74 0 N .314
18 -1.841 20790 431 248 34 5 139 92 38 13 544 156 40 149 378 105 -1.862 .83 0 N -1.841
19 -.273 20685 1188 717 34 5 1261 1024 38 14 544 156 40 1355 1305 1080 .189 .86 0 N -.273
20 -.199 20580 157 71 35 5 128 67 38 13 544 156 40 137 112 97 -.331 .85 0 N -.199

Total number of rows: 22575

Table truncated, full table size 1776 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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