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Sample GSM381092 Query DataSets for GSM381092
Status Public on Jun 11, 2009
Title Agilent-8439_1
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 4
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 4
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 .699 45220 2892 657 81 32 5423 1522 40 34 409 80 33 4595 3374 4484 .41 .86 0 .41
2 0 44688 81 26 81 24 54 34 39 34 426 120 33 45 0 0 0 -1 0 0
3 3 44156 84 24 83 24 48 30 38 31 398 120 32 40 2 4 .743 .03 0 .743
4 0 43624 80 23 80 23 47 27 38 33 459 120 32 39 0 0 0 .03 0 0
5 -.264 43092 84 23 78 23 44 27 38 32 399 120 32 37 11 3 -1.793 .03 0 -1.793
6 1.222 42560 81 25 78 24 48 28 39 31 466 120 33 40 5 4 -.381 .04 0 -.381
7 0 42028 81 23 81 24 50 33 39 35 447 120 33 42 0 0 0 .06 0 0
8 0 41496 81 23 81 24 54 34 40 32 471 120 33 45 0 0 0 .12 0 0
9 1.222 40964 85 25 82 25 48 35 39 35 398 120 33 40 5 4 -.381 .03 0 -.381
10 1.585 40432 82 22 79 22 51 34 41 36 400 120 34 43 5 5 -.166 .03 0 -.166
11 .737 39900 86 23 80 27 54 36 42 36 484 120 35 45 9 7 -.37 .17 0 -.37
12 3.459 39368 82 26 80 25 67 53 41 34 430 120 34 56 3 15 2.13 .14 0 2.13
13 -3.381 38836 3441 872 81 25 419 198 37 37 317 80 31 355 3852 333 -3.532 .82 0 -3.532
14 -2.756 38304 256 62 80 23 70 46 40 33 316 80 33 59 187 28 -2.742 .2 0 -2.742
15 -.436 37772 101 29 78 27 61 42 41 31 223 52 34 51 28 16 -.777 -1 0 -.777
16 1.131 37240 246 69 83 23 462 207 41 36 371 80 34 391 175 391 1.159 .83 0 1.159
17 2.459 36708 82 26 80 23 52 34 39 34 457 120 33 44 3 6 .712 .98 0 .712
18 .498 36176 97 39 80 24 68 61 39 35 463 120 33 57 20 23 .212 .13 0 .212
19 -1.083 35644 115 30 79 26 59 37 39 40 206 52 33 50 42 16 -1.328 .11 0 -1.328
20 .665 35112 107 34 78 25 93 83 38 32 239 52 32 78 32 48 .585 .3 0 .585

Total number of rows: 45220

Table truncated, full table size 3575 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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