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Sample GSM80427 Query DataSets for GSM80427
Status Public on May 01, 2007
Title FVB_MMTV_Neu_CA05_875A_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_CA05_875A
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_CA05_875A_CHURCHILL
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 .074 22575 78 28 46 11 82 41 59 34 521 156 68 95 26 27 -.245 .15 0 Y .074
2 .15 22470 69 22 46 11 75 40 58 36 544 156 67 87 18 20 -.201 .03 0 Y .15
3 1.599 22365 116 39 46 11 217 99 59 33 568 156 68 252 60 183 1.395 .73 0 N 1.599
4 -.032 22260 90 30 45 12 89 47 59 35 568 156 68 103 37 36 -.362 .21 0 N -.032
5 -.096 22155 905 408 46 12 818 399 58 35 544 156 67 951 835 781 .041 .96 0 N -.096
6 -2.829 22050 379 211 46 12 92 47 57 33 544 156 66 106 287 40 -3.059 .4 0 N -2.829
7 .263 21945 79 23 46 12 84 45 57 32 544 156 66 97 27 32 -.091 .17 0 Y .263
8 -1.228 21840 322 160 46 11 148 79 57 31 544 156 66 172 242 103 -1.381 .7 0 N -1.228
9 -.078 21735 73 24 45 11 75 36 57 32 568 156 66 87 23 21 -.415 .15 0 N -.078
10 .726 21630 104 40 46 12 124 66 56 34 568 156 65 144 48 80 .446 .53 0 N .726
11 .385 21525 243 120 46 11 262 138 58 34 544 156 67 304 175 229 .267 .86 0 N .385
12 -.402 21420 120 41 46 12 97 51 58 33 544 156 67 112 61 46 -.718 .33 0 N -.402
13 .446 21315 206 87 46 12 225 104 56 32 544 156 65 261 140 191 .293 .82 0 N .446
14 .136 21210 77 26 45 11 78 38 54 34 544 156 62 90 26 29 -.193 .2 0 Y .136
15 -.383 21105 495 209 44 11 350 174 54 34 568 156 62 406 417 319 -.39 .89 0 N -.383
16 .067 21000 80 29 45 11 82 38 57 33 568 156 66 95 28 30 -.271 .17 0 N .067
17 .127 20895 147 57 45 11 141 65 59 35 544 156 68 163 87 95 -.103 .62 0 N .127
18 -.607 20790 1563 895 46 12 1040 593 57 33 544 156 66 1209 1507 989 -.409 .96 0 N -.607
19 .304 20685 4062 2187 46 12 5624 3009 55 33 544 156 63 6539 4256 5254 .69 .98 0 N .304
20 .429 20580 337 147 46 11 383 193 55 34 544 156 63 445 266 358 .393 .89 0 N .429

Total number of rows: 22575

Table truncated, full table size 1854 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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