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Sample GSM69633 Query DataSets for GSM69633
Status Public on May 01, 2007
Title FVB_NJ_NORMAL_MAMMARYGLAND_CA04_677A
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_NJ_NORMAL_MAMMARYGLAND_CA04_677A
Organism Mus musculus
Characteristics mammary gland
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_NJ_NORMAL_MAMMARYGLAND_CA04_677A
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

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 -2.591 22575 81 23 38 8 48 16 42 16 550 156 48 55 39 6 -2.617 .11 0 Y -2.591
2 .217 22470 44 8 38 7 45 15 40 15 576 156 46 52 5 5 0 -1 0 Y .217
3 .129 22365 84 129 38 6 82 120 40 14 600 156 46 95 42 45 .091 .91 0 N .129
4 -.063 22260 47 9 38 11 48 16 41 14 600 156 47 55 8 7 -.17 .03 0 N -.063
5 -.421 22155 710 276 38 11 449 201 42 14 576 156 48 522 605 452 -.504 .93 0 N -.421
6 -1.055 22050 129 53 38 6 78 34 42 15 576 156 48 90 82 39 -1.114 .63 0 N -1.055
7 -1.398 21945 91 37 38 7 58 34 41 14 576 156 47 67 48 18 -1.407 .53 0 Y -1.398
8 -.842 21840 73 22 39 6 56 22 40 15 576 156 46 65 31 17 -.839 .28 0 N -.842
9 .217 21735 44 8 38 6 46 15 41 15 600 156 47 53 5 5 0 .08 0 N .217
10 -.148 21630 50 10 38 6 51 18 42 15 600 156 48 59 10 9 -.125 .19 0 N -.148
11 -.297 21525 57 13 38 6 54 21 41 13 576 156 47 62 17 14 -.342 .26 0 N -.297
12 21420 145 311 38 7 134 253 41 13 576 156 47 155 95 104 .013 .93 -100 N .128
13 -.01 21315 80 65 38 6 77 60 42 14 576 156 48 89 38 38 -.035 .81 0 N -.01
14 -3.071 21210 88 27 38 6 47 16 42 15 600 156 48 54 45 5 -3.059 .08 0 Y -3.071
15 -.889 21105 100 31 38 6 69 27 41 15 600 156 47 80 56 30 -.911 .51 0 N -.889
16 -.492 21000 47 9 38 7 46 16 41 15 576 156 47 53 7 5 -.584 -1 0 N -.492
17 -.011 20895 69 18 38 7 66 25 40 13 576 156 46 76 28 28 -.047 .47 0 N -.011
18 -.87 20790 381 185 38 8 188 93 41 15 576 156 47 218 303 166 -1.003 .89 0 N -.87
19 -.277 20685 1418 639 38 8 1005 494 43 16 576 156 50 1168 1268 1046 -.304 .93 0 N -.277
20 -.292 20580 116 41 38 6 93 43 41 15 600 156 47 108 70 57 -.355 .71 0 N -.292

Total number of rows: 22575

Table truncated, full table size 1758 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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