NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM69574 Query DataSets for GSM69574
Status Public on May 01, 2007
Title BALBc_NORMAL_MAMMARYGLAND_100992_SIMIN
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 BALBc_NORMAL_MAMMARYGLAND_100992
Organism Mus musculus
Characteristics mammary gland
Biomaterial provider Terry Van Dyke - UNC
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 BALBc_NORMAL_MAMMARYGLAND_100992_SIMIN
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 (2)
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
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 -1.017 22575 156 49 39 8 132 69 65 47 550 156 52 107 125 62 -1.089 .46 0 Y -1.017
2 .354 22470 67 20 39 8 111 91 63 47 576 156 51 90 32 41 .478 .94 0 Y .354
3 .857 22365 104 25 39 9 197 106 62 44 600 156 50 160 69 126 .759 .61 0 N .857
4 .562 22260 74 20 39 9 133 69 62 41 600 156 50 108 41 60 .729 .47 0 N .562
5 .34 22155 722 294 39 7 789 364 61 42 576 156 49 641 626 793 -.206 .95 0 N .34
6 -1.53 22050 332 142 39 7 162 114 63 44 576 156 51 131 289 100 -1.873 .56 0 N -1.53
7 -1.099 21945 148 51 39 8 126 94 66 45 576 156 53 102 118 55 -1.152 .42 0 Y -1.099
8 -.752 21840 162 72 40 9 144 85 62 41 576 156 50 117 129 77 -.865 .6 0 N -.752
9 .267 21735 68 15 40 9 108 58 63 39 600 156 51 87 32 38 .363 .3 0 N .267
10 1.618 21630 89 28 40 8 237 115 64 43 600 156 52 192 52 161 1.515 .69 0 N 1.618
11 1.364 21525 164 55 40 8 365 180 64 46 576 156 52 296 120 309 .977 .85 0 N 1.364
12 .495 21420 98 33 40 10 161 89 63 44 576 156 51 130 63 89 .446 .6 0 N .495
13 2.766 21315 112 33 40 10 528 227 60 42 576 156 48 429 70 478 2.404 .85 0 N 2.766
14 -.952 21210 176 59 40 9 140 161 61 44 594 156 49 113 144 74 -1.086 .45 0 Y -.952
15 -.92 21105 361 115 39 9 214 111 59 44 600 156 47 173 307 162 -1.355 .71 0 N -.92
16 .592 21000 77 18 40 8 135 71 59 39 582 156 47 109 43 65 .745 .45 0 N .592
17 2.428 20895 165 57 40 9 653 278 61 41 576 156 49 530 117 631 1.944 .91 0 N 2.428
18 -.996 20790 1450 752 40 9 663 345 61 43 576 156 49 539 1301 652 -1.523 .95 0 N -.996
19 .211 20685 2564 1103 40 10 2647 1196 61 42 576 156 49 2152 2374 2748 -.264 .98 0 N .211
20 1.908 20580 214 100 39 10 630 358 63 43 600 156 51 512 162 610 1.397 .9 0 N 1.908

Total number of rows: 22575

Table truncated, full table size 1847 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap