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Sample GSM1046493 Query DataSets for GSM1046493
Status Public on Nov 04, 2013
Title NA_MMTV_HRAS_4379-1_LI
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_HRAS_4379-1_LI
Organism Mus musculus
Characteristics sample: MMTV HRAS
Biomaterial provider Yi Li - Baylor College of Medicine
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 -7.173 22575 4357 2557 35 12 77 50 47 41 521 156 37 61 4326 29 -7.381 .24 0
2 .432 22470 50 17 35 12 67 48 48 39 544 156 38 53 14 19 0 .09 0
3 .839 22365 65 26 35 13 103 67 50 42 568 156 40 82 29 53 .485 .35 0
4 .285 22260 56 20 36 12 71 47 48 40 568 156 38 56 19 23 -.152 .08 0
5 -.341 22155 1442 722 37 24 1591 1037 50 40 544 156 40 1272 1656 1307 -.189 .87 0
6 -2.62 22050 284 149 36 23 85 56 48 43 544 156 38 68 237 38 -3.047 .24 0
7 .881 21945 36 13 34 24 59 42 45 41 544 156 36 47 3 7 2.459 .16 0
8 -1.439 21840 119 53 34 12 76 51 46 38 544 156 36 60 83 30 -1.826 .2 0
9 -.075 21735 53 19 35 12 66 46 50 42 568 156 40 52 17 16 -.584 .05 0
10 -.144 21630 66 27 35 11 79 52 51 43 568 156 40 63 30 28 -.431 .24 0
11 -.406 21525 130 62 35 12 114 72 48 42 544 156 38 91 91 68 -.842 .44 0
12 -.137 21420 69 29 35 12 78 55 47 38 544 156 37 62 34 30 -.444 .1 0
13 .838 21315 90 38 35 11 137 95 46 38 544 156 36 109 52 94 .408 .56 0
14 .291 21210 58 21 36 12 72 47 46 38 544 156 36 57 21 26 -.066 .04 0
15 .491 21105 266 132 35 26 356 223 45 39 570 156 36 284 226 317 .103 .85 0
16 .191 21000 52 18 34 26 64 42 45 41 570 156 36 51 17 19 -.264 .03 0
17 -.026 20895 111 46 35 13 115 75 46 39 544 156 36 92 73 71 -.44 .48 0
18 -.576 20790 910 484 35 12 739 496 46 41 544 156 36 591 950 637 -.657 .89 0
19 -.213 20685 5445 2973 36 56 9309 6149 49 91 544 156 39 7447 7618 6574 .454 .93 0
20 .145 20580 216 106 35 56 233 152 47 90 544 156 37 186 174 192 -.281 .79 0

Total number of rows: 22575

Table truncated, full table size 1718 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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