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Sample GSM662245 Query DataSets for GSM662245
Status Public on Aug 15, 2011
Title FVB_MMTV_Neu_110277_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 Cam Patterson - UNC
Extracted molecule total RNA
Extraction protocol Total RNA isolated by Trizol
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
Channel 2
Source name FVB_MMTV_Neu_110277_PEROU
Organism Mus musculus
Characteristics strain: FVB
tumor: mammary tumor
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Mini Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-576
Scan protocol scanned on Agilent scanner (model G2505B)
Description mammary tumor
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Jan 26, 2011
Last update date Jul 17, 2015
Contact name Charles M. Perou
E-mail(s) [email protected]
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 GPL4134
Series (2)
GSE27101 Comparative oncogenomics identifies breast tumors enriched in functional tumor initiating cells
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)
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 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 .147 1217 125 71 15 1692 235 38 14 69 12 42 1880 1308 1448 .682 .95 0
2 1.838 72 14 71 14 38 12 34 10 76 32 37 42 1 3 2.322 .93 0
3 0 70 16 71 13 37 14 32 14 72 32 35 41 0 0 0 .12 0
4 0 71 15 70 13 34 10 35 12 73 32 38 37 0 0 0 .03 0
5 0 71 15 72 13 37 13 33 11 76 32 36 41 0 0 0 .03 0
6 0 69 13 70 15 40 16 33 9 78 32 36 44 0 0 0 -1 0
7 0 73 18 73 13 37 14 34 10 78 32 37 41 0 0 0 .03 0
8 0 70 14 71 12 39 12 35 11 76 32 38 43 0 0 0 .08 0
9 0 68 11 68 14 42 13 36 10 76 32 40 46 0 0 0 -1 0
10 0 72 13 68 13 33 6 36 11 78 32 40 36 0 0 0 -1 0
11 0 70 14 72 12 44 19 36 13 76 32 40 48 0 0 0 .99 0
12 1.019 73 15 70 13 39 17 33 13 77 32 36 43 2 6 1.222 .98 0
13 -3.523 2177 506 76 11 252 61 36 17 46 12 40 280 2284 198 -3.133 .93 0
14 -2.457 179 22 72 12 47 13 34 12 54 12 37 52 87 15 -2.837 .35 0
15 .751 82 15 72 16 48 22 34 13 80 32 37 53 9 15 .678 .77 0
16 .54 159 22 74 17 111 33 32 15 47 12 35 123 67 98 .05 .82 0
17 2.502 72 14 70 14 46 43 35 13 79 32 38 51 1 11 2.7 .99 0
18 -.826 87 78 70 14 42 15 34 12 76 32 37 46 15 8 -.919 .89 0
19 0 90 23 73 15 34 10 34 12 76 32 37 37 0 0 0 .74 0
20 -.122 80 17 70 15 41 14 33 11 78 32 36 45 9 8 -.152 .96 0

Total number of rows: 45220

Table truncated, full table size 2703 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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