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Sample GSM361041 Query DataSets for GSM361041
Status Public on Jul 07, 2010
Title Mixed_Rb_9.Nov10.07_UHNC
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
Extraction protocol Qiagen Rneasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
Channel 2
Source name Mixed_Rb_9.Nov10.07_UHNC
Organism Mus musculus
Characteristics primary mammary tumor
Biomaterial provider Eldad Zacksenhaus - University of Toronto
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-124
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 Mixed_Rb_9.Nov10.07_UHNC
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Jan 15, 2009
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 GPL2881
Series (2)
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

Data table header descriptions
ID_REF Spot Reference ID
LOG_RAT2N_MEAN log2_ratio of channel 2 normalized over channel 1
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
VALUE same as UNF_VALUE but with flagged values removed
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 LOG_RAT2N_MEAN 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 VALUE CORR FLAG CONTROL UNF_VALUE
1 -.565 22575 91 17 54 14 71 32 42 23 420 52 35 60 27 38 .467 .22 0 Y .467
2 -1.392 22470 84 22 63 21 52 21 43 20 176 32 36 44 12 15 .319 .08 0 Y .319
3 .02 22365 123 31 53 13 123 54 40 21 654 120 33 104 67 85 .34 .61 0 N .34
4 -1 22260 90 27 54 14 62 27 41 20 635 120 34 52 25 29 .225 .23 0 N .225
5 -.072 22155 1622 397 56 16 1796 455 40 21 707 120 33 1522 2132 1289 -.726 .98 0 N -.726
6 -3.322 22050 273 54 54 14 65 29 40 20 670 120 33 55 210 26 -3.017 .34 0 N -3.017
7 0 21945 51 12 53 13 49 24 43 21 497 80 36 41 0 0 0 .1 0 Y 0
8 -2.146 21840 307 70 55 15 108 46 41 22 716 120 34 91 268 62 -2.096 .68 0 N -2.096
9 -.819 21735 92 24 62 20 63 23 43 20 176 32 36 53 20 29 .543 .06 0 N .543
10 -.226 21630 110 26 55 15 96 43 41 22 679 120 34 81 49 61 .333 .46 0 N .333
11 -.546 21525 128 28 55 15 100 45 41 22 671 120 34 84 68 63 -.11 .53 0 N -.11
12 -1.023 21420 113 27 54 14 77 34 43 96 725 120 36 65 49 40 -.283 .34 0 N -.283
13 .084 21315 171 39 54 13 190 77 44 99 670 120 37 161 124 136 .132 .78 0 N .132
14 -.868 21210 97 23 55 13 70 33 43 21 664 120 36 59 31 35 .152 .27 0 Y .152
15 .352 21105 304 75 54 15 417 122 41 21 708 120 34 353 296 316 .095 .93 0 N .095
16 -1 21000 92 23 54 13 64 30 42 22 629 120 35 54 27 30 .161 .28 0 N .161
17 1.436 20895 194 52 55 13 483 170 40 22 652 120 33 409 161 381 1.244 .92 0 N 1.244
18 -.031 20790 1602 166 55 15 1826 246 40 21 544 80 33 1547 2107 1311 -.685 .98 0 N -.685
19 .068 20685 2679 555 54 13 3285 644 40 21 655 120 33 2783 3703 2300 -.687 .98 0 N -.687
20 -.095 20580 290 61 55 15 299 101 40 19 712 120 33 253 272 223 -.286 .9 0 N -.286

Total number of rows: 22575

Table truncated, full table size 1870 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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