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Sample GSM69615 Query DataSets for GSM69615
Status Public on May 01, 2007
Title FVB_MMTV_Neu_CA01_431A_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_MMTV_Neu_CA01_431A
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_MMTV_Neu_CA01_431A_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 -4.136 22575 311 132 38 10 47 15 37 12 521 156 48 61 219 12 -4.381 .3 0 Y -4.136
2 -.22 22470 69 17 39 10 45 15 38 12 544 156 50 59 15 13 -1.737 .24 0 Y -.22
3 .509 22365 87 31 39 7 79 36 38 11 568 156 50 103 37 52 .143 .74 0 N .509
4 .12 22260 70 20 39 7 49 17 37 11 568 156 48 64 18 20 -.955 .3 0 N .12
5 -1.016 22155 910 406 40 7 501 238 37 11 544 156 48 659 903 446 -.51 .98 0 N -1.016
6 -2.184 22050 184 76 39 7 58 33 37 12 544 156 48 76 117 25 -2.373 .44 0 N -2.184
7 -4.159 21945 352 155 39 8 49 18 37 11 544 156 48 64 259 14 -4.293 .36 0 Y -4.159
8 -1.085 21840 158 62 39 8 77 33 37 11 544 156 48 101 100 47 -1.168 .74 0 N -1.085
9 .381 21735 69 19 40 11 51 17 37 12 568 156 48 67 17 22 -.61 .38 0 N .381
10 .246 21630 83 27 39 11 65 25 37 11 568 156 48 85 32 38 -.25 .56 0 N .246
11 .179 21525 96 31 39 8 77 32 37 12 544 156 48 101 44 50 -.105 .7 0 N .179
12 -.493 21420 90 27 39 8 55 19 37 12 544 156 48 72 35 25 -1.086 .44 0 N -.493
13 .459 21315 107 34 39 8 103 39 37 11 544 156 48 135 57 78 .355 .79 0 N .459
14 -4.457 21210 390 153 39 240 48 17 37 80 544 156 48 63 291 13 -4.54 .3 0 Y -4.457
15 -.11 21105 170 60 40 235 135 55 37 78 568 156 48 177 117 108 -.012 .85 0 N -.11
16 -.015 21000 71 18 39 8 49 17 38 12 568 156 50 64 18 18 -1.191 .25 0 N -.015
17 1.075 20895 123 44 39 8 180 82 37 12 544 156 48 236 75 159 1.162 .89 0 N 1.075
18 -.41 20790 944 434 39 9 793 373 37 11 544 156 48 1043 953 717 .136 .99 0 N -.41
19 -.509 20685 2454 1279 40 9 2094 1097 37 12 544 156 48 2755 2658 1867 .165 .99 0 N -.509
20 -.084 20580 226 88 40 8 193 85 38 12 544 156 50 253 174 164 .126 .92 0 N -.084

Total number of rows: 22575

Table truncated, full table size 1817 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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