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Sample GSM80456 Query DataSets for GSM80456
Status Public on May 01, 2007
Title BALB_p53het_IR_C1301_4_KOLLER
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 BALB_p53het_IR_C1301_4
Organism Mus musculus
Characteristics mammary tumor
Biomaterial provider Beverly Koller - 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 BALB_p53het_IR_C1301_4_KOLLER
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Oct 27, 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 -.262 22575 65 19 44 12 82 47 64 43 521 156 54 69 21 17 -.486 .1 0 Y -.262
2 .142 22470 61 16 45 10 83 46 65 43 544 156 55 70 16 17 -.092 .04 0 Y .142
3 -.078 22365 99 37 46 10 116 66 66 42 568 156 55 98 52 50 -.302 .36 0 N -.078
4 -.498 22260 68 19 46 10 84 52 68 44 568 156 57 71 22 15 -.653 .06 0 N -.498
5 -.979 22155 3923 2329 45 10 2939 1848 67 43 544 156 56 2490 4685 2377 -.671 .96 0 N -.979
6 -3.902 22050 561 300 45 10 101 59 64 40 544 156 54 85 534 35 -4.059 .34 0 N -3.902
7 .484 21945 62 19 46 10 85 50 62 43 544 156 52 72 16 22 .322 .14 0 Y .484
8 -1.389 21840 404 210 45 10 218 126 62 43 544 156 52 184 383 146 -1.442 .76 0 N -1.389
9 -.777 21735 61 17 45 10 75 45 66 41 568 156 55 63 15 9 -1 .11 0 N -.777
10 -.357 21630 94 33 45 12 103 61 65 43 568 156 55 87 48 38 -.615 .29 0 N -.357
11 1.139 21525 145 63 45 12 304 186 65 42 544 156 55 257 104 229 1.014 .82 0 N 1.139
12 -.023 21420 100 36 45 10 120 62 66 39 544 156 55 101 54 54 -.258 .43 0 N -.023
13 -.398 21315 137 59 45 10 133 78 62 39 544 156 52 112 92 70 -.617 .55 0 N -.398
14 -.04 21210 65 18 44 10 83 47 62 42 568 156 52 70 21 20 -.223 .08 0 Y -.04
15 .388 21105 638 351 44 10 1054 658 67 44 568 156 56 893 669 875 .495 .94 0 N .388
16 .03 21000 66 18 46 175 88 49 67 62 544 156 56 74 20 20 -.152 .71 0 N .03
17 .163 20895 150 70 46 175 183 108 61 61 544 156 51 155 106 119 0 .69 0 N .163
18 -1.174 20790 3790 2242 46 11 2456 1571 63 40 544 156 53 2081 4496 1992 -.884 .95 0 N -1.174
19 -.394 20685 4895 3301 47 12 5698 4102 65 42 544 156 55 4828 5990 4558 -.022 .96 0 N -.394
20 -.822 20580 324 158 47 10 238 138 61 43 568 156 51 201 294 166 -.884 .8 0 N -.822

Total number of rows: 22575

Table truncated, full table size 1871 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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