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Sample GSM381091 Query DataSets for GSM381091
Status Public on Jun 11, 2009
Title Agilent-8436_4
Sample type RNA
 
Channel 1
Source name Whole mouse total RNA
Organism Mus musculus
Characteristics reference sample: whole mouse total RNA
Biomaterial provider Cam Patterson-UNC-CH
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
Channel 2
Source name Mammary tumor from MMTV-ATX transgenic mouse
Organism Mus musculus
Characteristics tissue: mammary tumor from MMTV-ATX transgenic mouse 3
Biomaterial provider Gordon Mills
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-124
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software.
Description Mammary tumor from MMTV-ATX transgenic mouse 3
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Mar 16, 2009
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 GPL4134
Series (2)
GSE15263 Expression of autotaxin and lysophosphatidic acid receptors increases mammary tumorigenesis, invasion, and metastases
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
LOG_RAT2N_MEAN log2_ratio of channel 2 normalized over channel 1
SPOT spot number on array (GenePix)
CH1_MEAN channel 1 mean intensity
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
VALUE same as UNF_VALUE but with flagged values removed
CORR correlation coefficient among pixels
FLAG Spot flag. 0:not flagged; negative:Flagged as bad spots; positive:flagged as good spots
UNF_VALUE LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN

Data table
ID_REF LOG_RAT2N_MEAN 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 VALUE CORR FLAG UNF_VALUE
1 .184 45220 8212 1918 79 25 10232 1059 67 52 67 12 60 9301 9139 9046 -.015 .94 0 -.015
2 1.116 44688 82 17 76 22 75 51 61 45 74 32 55 68 9 8 -.112 .96 0 -.112
3 1.459 44156 85 20 73 21 82 73 46 41 72 32 41 74 16 26 .752 .03 0 .752
4 1 43624 88 23 79 18 73 37 53 42 72 32 48 66 13 13 .048 .15 0 .048
5 2.1 43092 81 17 74 18 73 49 40 48 71 32 36 66 9 23 1.209 .04 0 1.209
6 1.807 42560 88 22 76 20 96 59 50 49 70 32 45 87 15 35 1.184 .04 0 1.184
7 .249 42028 89 22 73 20 68 40 47 39 80 32 42 61 21 15 -.519 .23 0 -.519
8 -.347 41496 93 18 79 18 69 46 57 45 73 32 51 62 20 8 -1.348 .03 0 -1.348
9 0 40964 80 19 81 17 78 47 74 49 74 32 67 70 0 0 0 -1 0 0
10 0 40432 79 18 81 18 56 39 47 49 72 32 42 50 0 0 0 -1 0 0
11 -.633 39900 216 681 78 16 153 496 56 51 73 32 50 139 131 101 -.367 .97 0 -.367
12 1.16 39368 97 28 80 20 91 67 49 44 73 32 44 82 21 33 .634 .39 0 .634
13 -2.662 38836 6267 1827 77 20 1128 391 54 39 49 12 49 1025 6869 967 -2.827 .81 0 -2.827
14 -2.955 38304 539 69 82 19 118 54 53 33 53 12 48 107 450 65 -2.775 .41 0 -2.775
15 -.569 37772 120 41 77 19 87 48 56 45 79 32 50 79 50 26 -.936 .82 0 -.936
16 1.23 37240 459 73 78 18 1053 396 70 31 48 12 63 957 407 919 1.173 .92 0 1.173
17 .323 36708 1012 3140 81 25 1333 4660 51 60 63 32 46 1211 1018 1171 .202 .98 0 .202
18 .606 36176 104 40 81 18 84 59 46 55 76 32 41 76 28 30 .119 .75 0 .119
19 -1.293 35644 154 18 83 20 92 78 60 35 36 12 54 83 77 29 -1.421 .08 0 -1.421
20 .742 35112 134 26 79 23 155 68 53 40 34 12 48 140 53 105 .978 .5 0 .978

Total number of rows: 45220

Table truncated, full table size 3391 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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