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Sample GSM1046778 Query DataSets for GSM1046778
Status Public on Nov 04, 2013
Title FVB_MMTV-PyMT_118021_Non-treated
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_MMTV-PyMT_118021_Non-treated
Organism Mus musculus
Characteristics sample: MMTV PyMT
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 GPL11383
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 .289 1 35946 1794 16 9 39052 5598 37 20 10444 76 80 84895 33870 41388 1.239 -1 0
2 .5 2 29 16 17 10 46 21 37 20 8612 94 80 100 9 12 1 .29 0
3 -.076 3 25 11 17 10 39 23 37 20 7206 82 80 84 4 4 -.584 .46 0
4 .872 4 23 12 17 10 41 18 36 20 7178 88 78 89 4 7 1.459 .39 0
5 1.506 5 27 11 17 10 52 29 36 20 7284 86 78 113 7 22 2.129 .52 0
6 .863 6 23 11 17 10 40 22 36 19 7114 82 78 86 4 7 1 .33 0
7 -.586 7 26 10 17 10 37 17 36 19 7152 80 78 80 4 3 -1.586 .42 0
8 1.307 8 24 12 17 10 45 22 36 20 7164 86 78 97 5 13 1.926 .59 0
9 .696 9 23 11 17 10 40 20 36 20 7254 84 78 86 4 6 .678 -1 0
10 .522 10 24 11 17 10 40 17 36 20 7204 82 78 86 5 7 .415 .15 0
11 .03 11 26 14 17 10 40 23 36 20 7198 80 78 86 6 6 0 .36 0
12 0 12 24 11 17 10 35 16 37 20 7144 80 80 76 0 0 0 -1 0
13 .664 13 26 13 17 10 44 20 37 20 7270 84 80 95 6 10 .907 .25 0
14 .963 14 28 12 17 10 49 20 37 20 7252 84 80 106 8 17 1.379 .11 0
15 -1.22 15 29 15 17 10 38 17 37 20 7244 86 80 82 6 2 -2.322 -1 0
16 .544 16 24 10 16 9 42 23 37 20 7172 86 80 91 5 8 .874 .14 0
17 -1.094 17 27 14 16 9 38 19 37 20 7160 82 80 82 6 2 -2.171 .29 0
18 -.179 18 25 15 16 9 40 18 37 20 7140 86 80 86 6 5 -.223 .54 0
19 .49 19 26 13 16 9 43 22 36 21 7232 80 78 93 7 10 .907 .19 0
20 -1.671 20 26 15 16 10 37 19 37 21 7258 78 80 80 4 1 0 -1 0

Total number of rows: 180880

Table truncated, full table size 13061 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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