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Sample GSM381089 Query DataSets for GSM381089
Status Public on Jun 11, 2009
Title Agilent-8440_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 1
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 1
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 .665 45220 4349 1322 78 26 5395 1236 45 46 445 80 56 6829 4233 5397 .351 .97 0 .351
2 2.663 44688 80 25 77 23 56 35 41 39 431 120 51 70 5 7 .391 .03 0 .391
3 2.585 44156 81 23 78 23 54 34 40 35 427 120 50 68 5 7 .238 -1 0 .238
4 2.524 43624 83 26 79 189 58 47 40 288 485 120 50 73 6 10 .606 -1 0 .606
5 1.222 43092 80 25 74 24 50 35 39 36 497 120 49 63 10 6 -.759 .16 0 -.759
6 2.087 42560 83 25 75 25 66 41 39 33 173 32 49 83 10 20 .963 .03 0 .963
7 0 42028 76 24 76 22 54 37 38 35 437 120 48 68 0 0 0 .06 0 0
8 0 41496 76 23 77 23 59 46 41 33 417 120 51 74 0 0 0 .1 0 0
9 2.322 40964 82 24 78 22 55 36 39 36 442 120 49 69 7 9 .343 .09 0 .343
10 2.17 40432 82 24 78 22 53 34 39 37 468 120 49 67 7 7 .045 .07 0 .045
11 1.322 39900 82 25 78 24 47 27 39 38 445 120 49 59 8 3 -1.192 .03 0 -1.192
12 .53 39368 85 25 76 25 50 35 40 41 464 120 50 63 14 6 -1.235 -1 0 -1.235
13 -3.381 38836 3820 1007 78 24 323 154 40 41 304 80 50 408 3261 324 -3.328 .79 0 -3.328
14 -.111 38304 292 67 77 23 194 109 37 34 319 80 46 245 172 196 .188 .67 0 .188
15 .598 37772 119 30 84 24 81 72 39 34 220 32 49 102 34 42 .295 .08 0 .295
16 1.029 37240 272 68 78 23 352 150 39 36 338 80 49 445 155 389 1.323 .77 0 1.323
17 2.807 36708 80 24 77 22 57 43 41 37 463 120 51 72 5 8 .534 -1 0 .534
18 1.138 36176 85 22 75 24 57 39 40 36 439 120 50 72 13 12 -.17 .04 0 -.17
19 -.678 35644 111 38 79 24 54 34 38 33 444 120 48 68 36 14 -1.374 -1 0 -1.374
20 1.181 35112 96 26 81 26 70 58 43 34 152 32 54 88 17 22 .373 .06 0 .373

Total number of rows: 45220

Table truncated, full table size 3576 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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