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Sample GSM381095 Query DataSets for GSM381095
Status Public on Jun 11, 2009
Title Agilent-9441_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-LPA1 transgenic mouse
Organism Mus musculus
Characteristics tissue: mammary tumor from MMTV-LPA1 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-LPA1 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 1.571 45220 15421 2469 50 13 39341 11673 57 116 67 12 66 45745 19711 30634 .636 .96 0 .636
2 0 44688 63 16 53 12 48 17 39 59 34 12 45 55 9 9 .045 1 0 .045
3 -.808 44156 54 14 47 10 42 12 38 11 77 32 44 48 6 4 -.641 -1 0 -.641
4 -.584 43624 54 11 51 12 40 10 38 12 76 32 44 46 2 2 -.461 -1 0 -.461
5 0 43092 54 11 49 12 40 10 42 11 78 32 48 46 0 0 0 .23 0 0
6 0 42560 57 10 51 12 39 12 40 11 78 32 46 45 0 0 0 .08 0 0
7 0 42028 49 11 49 11 40 11 37 10 76 32 43 46 0 0 0 -1 0 0
8 0 41496 51 11 50 10 38 10 40 9 76 32 46 44 0 0 0 .07 0 0
9 0 40964 54 13 52 10 39 10 37 11 81 32 43 45 1 2 .112 .17 0 .112
10 0 40432 51 10 49 12 39 6 39 8 79 32 45 45 0 0 0 -1 0 0
11 1.585 39900 52 9 50 11 44 13 39 16 79 32 45 51 1 5 1.46 1 0 1.46
12 -.808 39368 61 13 47 11 46 12 39 16 83 32 45 53 13 7 -.801 .89 0 -.801
13 -1.644 38836 1459 137 48 10 429 127 41 8 50 12 47 498 1341 408 -1.716 .87 0 -1.716
14 1.1 38304 140 19 49 13 208 55 40 11 52 12 46 241 81 186 1.19 .84 0 1.19
15 0 37772 63 19 49 10 51 21 39 14 84 32 45 59 13 12 -.011 .64 0 -.011
16 1.888 37240 249 40 45 12 687 165 37 10 49 12 43 798 187 707 1.917 .95 0 1.917
17 2.399 36708 81 174 52 12 171 661 39 10 84 32 45 198 25 147 2.508 .99 0 2.508
18 1 36176 52 11 51 11 42 13 40 11 82 32 46 48 0 2 1.092 .98 0 1.092
19 -3.458 35644 125 24 48 11 44 15 38 11 46 12 44 51 70 6 -3.443 .19 0 -3.443
20 -.264 35112 55 14 49 11 43 14 39 9 80 32 45 50 5 4 -.423 .9 0 -.423

Total number of rows: 45220

Table truncated, full table size 3219 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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