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Sample GSM69646 Query DataSets for GSM69646
Status Public on May 01, 2007
Title FVB_Wap_Myc_CA02_540B_spindloid_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_Wap_Myc_CA02_540B_spindloid
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_Wap_Myc_CA02_540B_spindloid_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 -4.95 22575 451 207 38 408 53 19 39 68 521 156 38 52 422 13 -4.878 .89 0 Y -4.95
2 .023 22470 61 15 39 10 48 15 40 13 544 156 39 47 13 13 -1.458 .24 0 Y .023
3 .14 22365 91 29 38 11 94 37 40 13 568 156 39 93 50 56 .027 .73 0 N .14
4 .196 22260 65 16 38 8 56 19 39 13 568 156 38 55 20 22 -.667 .35 0 N .196
5 -1.109 22155 1093 497 38 104 714 338 39 16 544 156 38 706 1239 574 -.66 .98 0 N -1.109
6 -3.052 22050 240 102 38 104 65 25 40 16 544 156 39 64 204 24 -3.012 .65 0 N -3.052
7 -4.737 21945 459 215 38 7 57 20 40 14 544 156 39 56 436 16 -4.644 .38 0 Y -4.737
8 -1.694 21840 155 59 38 15 75 32 39 14 544 156 38 74 116 36 -1.699 .64 0 N -1.694
9 .448 21735 64 16 39 14 57 20 38 13 568 156 37 56 18 25 -.396 .39 0 N .448
10 21630 270 2272 38 8 343 2819 39 14 568 156 38 339 259 272 .375 1 -100 N .07
11 -.296 21525 101 32 38 8 88 32 40 14 544 156 39 87 60 49 -.392 .74 0 N -.296
12 .27 21420 86 27 38 7 91 159 39 13 544 156 38 90 45 54 .115 .51 0 N .27
13 .549 21315 116 35 38 7 167 64 40 14 544 156 39 165 82 120 .692 .87 0 N .549
14 -4.651 21210 494 206 39 7 60 23 40 13 544 156 39 59 478 19 -4.506 .43 0 Y -4.651
15 -.038 21105 228 81 38 7 266 105 40 13 568 156 39 263 209 204 .238 .95 0 N -.038
16 .11 21000 69 19 38 7 61 23 40 13 568 156 39 60 24 26 -.563 .42 0 N .11
17 .11 20895 116 38 39 7 128 59 39 13 544 156 38 126 79 86 .193 .82 0 N .11
18 -.7 20790 915 429 39 7 780 368 39 13 544 156 38 772 1027 632 -.255 .99 0 N -.7
19 -.084 20685 2395 1229 38 7 3462 1824 39 13 544 156 38 3427 2924 2758 .524 1 0 N -.084
20 -.003 20580 176 65 38 7 201 87 38 13 544 156 37 199 150 149 .231 .9 0 N -.003

Total number of rows: 22575

Table truncated, full table size 1814 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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