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Sample GSM80450 Query DataSets for GSM80450
Status Public on May 01, 2007
Title FVB_MMTV_Neu_69331_USARY
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_69331
Organism Mus musculus
Characteristics mammary tumor
Biomaterial provider Charles Perou - 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 FVB_MMTV_Neu_69331_USARY
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 -2.246 22575 341 144 67 20 79 34 47 24 521 156 51 86 203 42 -2.966 .43 0 Y -2.246
2 .305 22470 130 49 67 23 63 26 46 24 544 156 50 69 29 36 -1.727 .2 0 Y .305
3 1.092 22365 223 90 66 24 345 180 45 22 568 156 49 379 148 316 1.072 .89 0 N 1.092
4 .44 22260 156 57 70 45 93 47 47 24 568 156 51 102 54 73 -.754 .48 0 N .44
5 -.661 22155 5808 3028 71 46 6206 3373 46 24 544 156 50 6819 7474 4728 .239 .99 0 N -.661
6 -2.814 22050 582 304 70 19 105 52 46 23 544 156 50 115 460 65 -2.977 .68 0 N -2.814
7 -2.023 21945 335 162 70 19 84 39 46 22 544 156 50 92 202 49 -2.662 .5 0 Y -2.023
8 -.677 21840 410 232 69 19 254 151 47 21 544 156 51 279 335 210 -.58 .91 0 N -.677
9 .482 21735 136 45 68 39 73 34 47 24 568 156 51 80 35 49 -1.231 .27 0 N .482
10 .194 21630 186 77 68 38 121 65 46 24 568 156 50 132 87 100 -.525 .67 0 N .194
11 .446 21525 253 106 71 20 258 140 45 24 544 156 49 283 168 229 .363 .86 0 N .446
12 -.025 21420 189 83 73 20 103 57 47 23 544 156 51 113 81 79 -.905 .6 0 N -.025
13 .937 21315 272 111 72 19 423 231 47 24 544 156 51 464 198 379 1.046 .89 0 N .937
14 -2.44 21210 370 172 72 25 77 35 46 25 544 156 50 84 223 41 -3.133 .44 0 Y -2.44
15 -.151 21105 846 378 72 24 948 464 46 25 568 156 50 1041 880 793 .356 .97 0 N -.151
16 .251 21000 155 58 71 20 81 40 47 22 568 156 51 89 48 58 -1.146 .42 0 N .251
17 1.153 20895 334 152 70 19 700 379 48 23 544 156 52 769 278 618 1.441 .94 0 N 1.153
18 -.456 20790 3474 1917 72 21 4108 2292 48 23 544 156 52 4514 4352 3173 .392 .99 0 N -.456
19 -.303 20685 8318 4512 74 22 11528 6177 46 25 544 156 50 12668 10804 8760 .614 .99 0 N -.303
20 -.018 20580 654 370 72 21 751 462 45 23 544 156 49 825 644 637 .415 .96 0 N -.018

Total number of rows: 22575

Table truncated, full table size 1917 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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