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Sample GSM873947 Query DataSets for GSM873947
Status Public on Aug 21, 2012
Title FVB_C57Bl6_C3(1)_Tag_117277T1_HERSCH
Sample type RNA
 
Channel 1
Source name Whole Mouse Reference RNA
Organism Mus musculus
Characteristics reference: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups
Biomaterial provider Charles Perou - UNC
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen RNeasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
Channel 2
Source name FVB_C57Bl6_C3(1)_Tag_117277T1_HERSCH
Organism Mus musculus
Characteristics tumor: Untreated C3(1)-Tag mammary tumor
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-125
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software
Description Mammary Tumor
Data processing Data for both channels were Lowess-normalized and then the log(2) ratio was taken
 
Submission date Feb 10, 2012
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)
GSE35722 Combined PI3K/mTOR and MEK Inhibition Provides Broad Anti-Tumor Activity in Faithful Murine Cancer Models
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
VALUE log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN)
SPOT spot number on array
CH1_MEAN
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 channel 2 normalized over channel 1 (global normalization)
CORR correlation coefficient among pixels
FLAG Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots

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
1 .404 22575 126 48 82 69 98 56 60 54 521 156 53 87 35 47 -.371 .14 0
2 -.583 22470 120 39 82 48 72 41 58 48 544 156 51 64 28 18 -1.548 -1 0
3 -.045 22365 150 47 81 29 113 58 61 39 568 156 54 100 60 58 -.584 .27 0
4 .28 22260 120 42 83 33 89 55 63 42 568 156 56 79 28 34 -.685 .1 0
5 -1.454 22155 1723 687 83 32 820 391 60 46 544 156 53 732 1847 674 -1.272 .9 0
6 -2.276 22050 394 201 83 32 126 75 60 45 544 156 53 112 315 65 -2.396 .41 0
7 1.133 21945 87 34 83 285 79 44 65 52 544 156 58 70 5 11 1.585 .05 0
8 -1.878 21840 221 78 83 284 95 60 65 53 544 156 58 84 123 33 -2.411 .1 0
9 -.325 21735 129 42 85 29 81 53 61 46 568 156 54 72 33 26 -1.29 .08 0
10 .064 21630 136 48 82 30 100 58 61 47 568 156 54 89 44 46 -.626 .2 0
11 -.547 21525 216 65 82 33 145 76 58 45 544 156 51 129 130 89 -.781 .42 0
12 -.184 21420 147 51 84 33 100 59 60 43 544 156 53 89 53 47 -.808 .13 0
13 .164 21315 234 71 82 30 241 116 60 38 544 156 53 215 156 175 .092 .63 0
14 .015 21210 135 48 83 31 97 56 62 41 544 156 55 86 42 42 -.747 .15 0
15 .474 21105 372 150 81 39 532 368 60 41 568 156 53 474 314 436 .533 .74 0
16 -.191 21000 132 45 80 39 87 51 58 39 568 156 51 77 41 36 -1 .09 0
17 .082 20895 198 72 86 31 172 97 58 43 544 156 51 153 109 116 -.134 .47 0
18 -.903 20790 1319 560 85 30 888 409 58 43 544 156 51 792 1383 740 -.737 .92 0
19 -1.401 20685 5058 2307 80 30 2774 1311 60 43 544 156 53 2476 5973 2261 -1.038 .93 0
20 -.291 20580 381 142 81 29 341 165 59 42 544 156 52 304 321 262 -.252 .8 0

Total number of rows: 22575

Table truncated, full table size 1739 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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