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Sample GSM1046313 Query DataSets for GSM1046313
Status Public on Nov 04, 2013
Title BALB/c_p53null_9263-3_transplant_135908
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 BALB/c_p53null_9362-2_transplant_135908
Organism Mus musculus
Characteristics sample: p53null
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 -.306 1 105122 4588 16 10 81897 8118 37 21 10356 78 84 186129 103134 83426 .824 -1 0
2 1.245 2 35 17 17 10 58 33 37 21 8472 82 84 131 13 31 1.467 .64 0
3 .097 3 33 15 17 11 44 24 37 21 7054 80 84 100 10 11 .193 .28 0
4 1.767 4 27 13 17 10 53 25 37 21 7138 78 84 120 7 24 2.17 .37 0
5 1.143 5 26 13 17 11 46 30 38 20 7106 76 86 104 6 13 1.362 .64 0
6 1.909 6 24 14 17 11 47 22 38 20 7062 82 86 106 4 16 2.322 .38 0
7 1.035 7 29 19 17 11 49 25 38 21 7070 84 86 111 8 16 1.322 -1 0
8 .187 8 32 22 17 11 45 19 38 21 7188 86 86 102 10 11 .3 .57 0
9 .002 9 27 16 17 11 41 16 38 21 7194 84 86 93 5 5 -.193 .28 0
10 .37 10 29 16 17 11 44 16 38 21 7220 68 86 100 7 10 .485 -1 0
11 -.028 11 33 18 17 11 44 21 38 21 7192 68 86 100 10 10 0 -1 0
12 .2 12 27 14 17 11 42 24 39 21 7268 82 88 95 5 6 0 .09 0
13 .627 13 29 15 17 11 45 23 38 20 7054 72 86 102 7 12 .678 .66 0
14 .385 14 33 17 18 11 47 21 38 20 7020 82 86 106 10 13 .515 .52 0
15 .52 15 31 17 18 11 47 22 39 21 7134 88 88 106 8 12 .71 .42 0
16 1.846 16 24 12 18 11 45 26 38 20 7296 80 86 102 3 13 2 -1 0
17 2.392 17 23 13 18 11 49 26 38 21 7182 80 86 111 3 18 2.644 -1 0
18 .687 18 37 20 18 11 53 28 38 20 7004 86 86 120 13 22 1 -1 0
19 .856 19 39 20 18 11 57 25 38 20 7110 82 86 129 15 27 1.178 .39 0
20 .13 20 33 17 17 11 44 21 37 20 7050 74 84 100 10 11 .3 .21 0

Total number of rows: 180880

Table truncated, full table size 13386 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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