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Sample GSM381096 Query DataSets for GSM381096
Status Public on Jun 11, 2009
Title Agilent-8440_2
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-LPA1 transgenic mouse
Organism Mus musculus
Characteristics tissue: mammary tumor from MMTV-LPA1 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-LPA1 transgenic mouse 3
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 .468 45220 3638 559 78 24 5951 1166 43 34 391 80 35 4959 4732 4444 -.09 .97 0 -.09
2 0 44688 81 23 81 24 48 34 40 37 425 120 33 40 0 0 0 .12 0 0
3 1.875 44156 84 25 81 23 52 39 39 32 400 120 32 43 5 7 .364 .04 0 .364
4 2.17 43624 81 23 79 25 51 32 40 35 453 120 33 42 4 5 .356 -1 0 .356
5 1.807 43092 82 26 80 24 47 26 39 33 401 120 32 39 4 3 -.302 -1 0 -.302
6 0 42560 80 24 80 23 50 32 39 31 403 120 32 41 0 0 0 -1 0 0
7 1.138 42028 82 24 77 22 52 31 39 31 401 120 32 43 8 7 -.054 .06 0 -.054
8 2.322 41496 80 23 78 24 50 30 38 31 400 120 31 41 4 5 .535 -1 0 .535
9 2.585 40964 81 23 79 23 56 36 41 32 459 120 34 46 3 7 .995 .05 0 .995
10 3 40432 79 22 78 24 50 34 40 34 401 120 33 41 2 4 .721 .08 0 .721
11 .485 39900 83 25 78 24 49 28 40 34 465 120 33 40 8 5 -.815 -1 0 -.815
12 -.613 39368 131 265 79 23 81 149 40 33 432 120 33 67 54 38 -.501 .6 0 -.501
13 -3.54 38836 3711 802 76 23 412 174 39 29 332 80 32 343 4271 317 -3.75 .84 0 -3.75
14 -2.766 38304 274 82 77 23 75 51 40 33 388 80 33 62 195 35 -2.471 .21 0 -2.471
15 .043 37772 112 30 79 25 80 52 39 39 226 52 32 66 36 37 .059 .16 0 .059
16 1.593 37240 251 75 78 23 664 252 38 35 312 80 31 553 180 599 1.73 .87 0 1.73
17 0 36708 83 26 76 22 48 29 40 44 434 120 33 40 11 4 -1.334 .28 0 -1.334
18 .737 36176 88 25 79 23 61 38 42 47 482 120 35 50 12 14 .205 .04 0 .205
19 -1.857 35644 107 35 78 25 51 32 41 33 449 120 34 42 36 7 -2.197 .04 0 -2.197
20 2.503 35112 89 20 80 24 101 59 40 31 162 32 33 84 10 51 2.289 .11 0 2.289

Total number of rows: 45220

Table truncated, full table size 3585 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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