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Sample GSM1046483 Query DataSets for GSM1046483
Status Public on Nov 04, 2013
Title FVB_MMTV_Aib1_T34_MBROWN
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_Aib1_T34_MBROWN
Organism Mus musculus
Characteristics sample: MMTV Aib1
Biomaterial provider Myles Brown - Dana-Farber Cancer Institute
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 GPL10732
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 -.564 22575 122 45 54 17 50 18 39 12 521 156 40 52 33 22 -2.506 .28 0
2 -.693 22470 121 46 55 17 47 17 39 12 544 156 40 48 29 18 -3.047 .13 0
3 -.074 22365 132 53 53 19 75 30 39 13 568 156 40 78 54 51 -1.056 .57 0
4 -.794 22260 137 190 53 20 55 64 39 13 568 156 40 57 48 27 -2.308 .87 0
5 -2.113 22155 1367 723 53 18 485 259 39 13 544 156 40 505 1592 368 -1.498 .96 0
6 -2.729 22050 279 139 53 17 59 23 39 14 544 156 40 61 173 26 -3.427 .44 0
7 -.391 21945 116 43 53 20 49 15 38 44 544 156 39 51 30 22 -2.396 .28 0
8 -2.714 21840 244 104 54 20 52 17 39 44 544 156 40 54 127 19 -3.756 .3 0
9 -.564 21735 121 47 53 17 50 18 39 13 568 156 40 52 33 22 -2.506 .19 0
10 .096 21630 133 59 53 17 85 38 39 13 568 156 40 88 58 62 -.737 .67 0
11 .242 21525 168 66 54 16 154 69 39 14 544 156 40 160 105 124 .075 .83 0
12 -.02 21420 131 53 54 18 76 32 40 14 544 156 41 79 53 52 -1.017 .56 0
13 -.225 21315 159 60 54 19 99 38 39 13 544 156 40 103 85 73 -.737 .7 0
14 -.339 21210 113 39 53 17 49 17 39 13 544 156 40 51 27 21 -2.45 .24 0
15 1.041 21105 227 104 54 16 470 266 40 13 568 156 41 489 190 391 1.373 .92 0
16 -.462 21000 119 45 54 17 51 19 40 14 568 156 41 53 31 22 -2.434 .27 0
17 .095 20895 152 61 53 18 114 51 39 13 544 156 40 118 83 89 -.344 .76 0
18 -1.385 20790 647 377 55 17 341 205 39 13 544 156 40 355 683 261 -.911 .94 0
19 -.373 20685 3137 1825 54 17 4143 2423 38 12 544 156 39 4315 4047 3126 .472 .99 0
20 -.557 20580 225 98 54 17 148 72 39 12 544 156 40 154 165 112 -.584 .84 0

Total number of rows: 22575

Table truncated, full table size 1714 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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