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Sample GSM381101 Query DataSets for GSM381101
Status Public on Jun 11, 2009
Title Agilent-9441_3
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-LPA2 transgenic mouse
Organism Mus musculus
Characteristics tissue: mammary tumor from MMTV-LPA2 transgenic mouse 2
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-LPA2 transgenic mouse 2
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Mar 17, 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 1.249 45220 16368 8541 45 519 33423 10154 60 292 62 12 69 38863 21515 25311 .234 .91 0 .234
2 .223 44688 50 12 44 9 44 19 38 40 75 32 44 51 5 6 .135 .95 0 .135
3 3.17 44156 46 8 45 9 46 18 38 10 35 12 44 53 0 8 3.102 .07 0 3.102
4 0 43624 48 10 43 8 42 11 37 10 73 32 43 48 4 5 .127 .25 0 .127
5 -1.221 43092 49 11 42 8 42 15 39 10 70 32 45 48 6 3 -1.1 .04 0 -1.1
6 -.415 42560 53 7 41 10 45 13 37 10 36 12 43 52 11 8 -.422 .03 0 -.422
7 0 42028 46 10 46 8 36 10 42 16 76 32 48 41 0 0 0 .07 0 0
8 .678 41496 49 12 44 8 45 10 38 11 76 32 44 52 4 7 .62 -1 0 .62
9 -1.221 40964 49 13 42 8 40 13 37 11 76 32 43 46 6 3 -1.1 .03 0 -1.1
10 -.584 40432 46 10 43 8 39 12 37 12 78 32 43 45 2 2 -.489 .11 0 -.489
11 -2.065 39900 89 217 43 9 49 24 39 12 75 32 45 56 42 10 -1.977 .92 0 -1.977
12 -.54 39368 78 14 46 7 57 13 38 13 34 12 44 66 29 20 -.511 .19 0 -.511
13 -1.938 38836 1837 598 46 16 442 151 39 9 48 12 45 513 1750 412 -2.086 .81 0 -2.086
14 1.509 38304 186 33 42 9 390 78 37 9 52 12 43 453 130 388 1.573 .81 0 1.573
15 .848 37772 60 18 45 9 59 35 36 10 77 32 41 68 13 24 .826 .69 0 .826
16 .82 37240 241 130 45 9 335 189 37 13 83 32 43 389 178 327 .878 .76 0 .878
17 3.17 36708 46 11 45 9 49 19 41 13 74 32 47 56 0 8 3.102 .88 0 3.102
18 -.678 36176 53 14 45 10 43 14 39 12 74 32 45 50 7 4 -.868 .68 0 -.868
19 -4.293 35644 162 31 44 8 44 10 39 13 55 12 45 51 108 5 -4.322 .15 0 -4.322
20 .363 35112 51 11 44 10 47 18 39 10 80 32 45 54 6 8 .339 .86 0 .339

Total number of rows: 45220

Table truncated, full table size 3225 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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