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Sample GSM80442 Query DataSets for GSM80442
Status Public on May 01, 2007
Title BALB_p53het_IR_C1301_1_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_1
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_1_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 .448 22575 65 18 44 8 81 46 56 33 521 156 62 90 19 26 .415 .22 0 Y .448
2 .15 22470 59 15 45 9 73 35 58 32 544 156 64 81 13 15 .28 .12 0 Y .15
3 .21 22365 118 46 46 94 121 66 57 35 568 156 63 134 63 73 -.02 .17 0 N .21
4 .349 22260 71 21 46 94 86 42 59 34 568 156 65 95 23 29 .263 .03 0 N .349
5 -.662 22155 3913 1981 47 10 2855 1616 59 32 544 156 65 3172 4135 2613 -.315 .95 0 N -.662
6 -3.082 22050 505 264 46 9 98 54 54 33 544 156 60 108 413 48 -3.252 .43 0 N -3.082
7 .693 21945 65 18 45 9 85 45 57 34 544 156 63 94 18 30 .632 .22 0 Y .693
8 -1.862 21840 368 167 44 9 130 72 57 33 544 156 63 144 293 80 -2 .62 0 N -1.862
9 .532 21735 58 14 45 9 73 38 55 32 568 156 61 81 12 18 .621 .03 0 N .532
10 .124 21630 92 31 45 9 95 50 55 30 568 156 61 105 41 45 -.095 .25 0 N .124
11 .679 21525 135 51 45 32 169 91 56 32 544 156 62 187 79 127 .474 .62 0 N .679
12 -.903 21420 152 691 45 31 100 49 56 34 544 156 62 111 93 50 -1.127 .05 0 N -.903
13 .317 21315 164 63 45 9 176 103 58 36 544 156 64 195 106 132 .139 .65 0 N .317
14 .303 21210 65 17 45 9 80 46 58 35 544 156 64 88 18 23 .263 .17 0 Y .303
15 .874 21105 610 309 45 38 1039 629 55 35 568 156 61 1154 550 1009 .952 .93 0 N .874
16 .213 21000 64 17 45 39 76 39 56 35 568 156 62 84 18 20 .212 .06 0 N .213
17 .286 20895 171 71 44 15 182 103 58 35 544 156 64 202 113 138 .12 .72 0 N .286
18 .886 20790 3151 1792 45 12 6879 4216 56 35 544 156 62 7643 3386 6258 1.287 .96 0 N .886
19 .067 20685 4898 2643 46 9 6207 3963 57 34 544 156 63 6896 5336 5591 .494 .95 0 N .067
20 -.096 20580 424 201 46 9 369 205 57 33 544 156 63 410 355 332 -.123 .89 0 N -.096

Total number of rows: 22575

Table truncated, full table size 1843 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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