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Sample GSM1046934 Query DataSets for GSM1046934
Status Public on Nov 04, 2013
Title FVB_Wap_Myc_117318_bRep_PEROU
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_Wap_Myc_117318_bRep_PEROU
Organism Mus musculus
Characteristics sample: Wap Myc
Biomaterial provider Charles Perou - UNC
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 Nov 29, 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)
GSE42640 Transcriptomic Classification of Genetically Engineered Mouse Models of Breast Carcinoma Identifies Human Subtype Counterparts
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 -6.73 22575 1867 1043 46 22 63 39 48 32 550 156 46 61 1702 16 -6.966 .11 0
2 .286 22470 52 11 45 21 61 35 47 33 576 156 45 59 8 10 1 -1 0
3 .379 22365 67 16 45 9 77 43 48 33 600 156 46 74 22 28 .348 .21 0
4 .363 22260 53 12 45 10 64 38 48 31 600 156 46 62 9 12 1 .05 0
5 -.904 22155 636 341 47 28 366 226 54 48 576 156 52 355 586 313 -.96 .83 0
6 -3.081 22050 206 103 47 30 68 45 52 58 576 156 50 66 146 17 -3.308 .12 0
7 0 21945 45 8 45 15 57 33 46 45 576 156 44 55 0 0 0 .1 0
8 .218 21840 70 19 46 10 74 44 46 32 576 156 44 71 24 27 .17 .21 0
9 -1.272 21735 53 11 46 10 52 30 46 30 600 156 44 50 10 4 -.223 .03 0
10 .394 21630 70 21 46 9 77 56 46 31 600 156 44 74 23 31 .322 .26 0
11 -.828 21525 126 48 46 9 83 53 45 33 576 156 43 80 73 41 -1.111 .33 0
12 .254 21420 68 17 46 9 72 53 45 31 576 156 43 69 22 26 .241 .15 0
13 .524 21315 99 33 46 13 109 69 45 35 576 156 43 105 48 69 .227 .49 0
14 .521 21210 57 13 46 15 66 38 45 292 576 156 43 64 12 18 .933 .13 0
15 -.906 21105 174 77 45 13 103 62 46 286 600 156 44 100 117 62 -1.204 .51 0
16 .23 21000 54 11 45 11 61 34 45 34 600 156 43 59 11 12 .83 .06 0
17 .255 20895 105 36 45 9 105 61 45 35 576 156 43 101 54 65 -.048 .49 0
18 -2.295 20790 607 330 45 9 149 91 44 33 576 156 42 144 538 109 -2.466 .69 0
19 -.87 20685 1614 894 46 10 1037 572 45 35 576 156 43 1006 1686 922 -.704 .94 0
20 -.182 20580 158 67 46 10 129 77 47 36 576 156 45 125 102 89 -.486 .58 0

Total number of rows: 22575

Table truncated, full table size 1643 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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