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Sample GSM381108 Query DataSets for GSM381108
Status Public on Jun 11, 2009
Title Agilent-9440_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-LPA3 transgenic mouse
Organism Mus musculus
Characteristics tissue: mammary tumor from MMTV-LPA3 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-LPA3 transgenic mouse 4
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 1.085 45220 15609 9993 47 8 29409 17109 37 15 106 32 41 33043 21733 21031 -.047 .91 0 -.047
2 -1.322 44688 52 12 47 9 37 10 35 9 68 32 39 41 4 2 -1.117 1 0 -1.117
3 -1 44156 52 10 46 7 36 10 33 7 72 32 37 40 5 3 -.78 .11 0 -.78
4 0 43624 53 11 48 9 36 12 32 7 71 32 35 40 4 4 -.1 .03 0 -.1
5 1 43092 51 9 50 8 36 9 34 8 72 32 38 40 0 2 1.164 .22 0 1.164
6 1 42560 48 9 46 8 35 7 32 6 72 32 35 39 1 3 .777 .13 0 .777
7 1.585 42028 48 10 47 9 36 8 33 9 71 32 37 40 0 3 1.759 .11 0 1.759
8 0 41496 49 9 47 9 34 6 34 7 71 32 38 38 0 0 0 .13 0 0
9 0 40964 51 10 44 8 35 6 35 10 72 32 39 39 0 0 0 .05 0 0
10 0 40432 50 9 46 8 33 6 33 8 71 32 37 37 0 0 0 .22 0 0
11 0 39900 53 12 48 9 39 11 34 12 75 32 38 43 4 5 .228 .7 0 .228
12 1.98 39368 103 26 47 10 228 81 32 11 51 12 35 256 49 222 2.174 .69 0 2.174
13 -.889 38836 1558 917 47 7 760 637 33 7 84 32 37 853 1590 690 -1.204 .64 0 -1.204
14 -2.351 38304 152 19 50 8 51 27 33 10 53 12 37 57 86 21 -2.023 .23 0 -2.023
15 -.502 37772 64 20 47 10 44 17 33 9 82 32 37 49 15 12 -.34 .67 0 -.34
16 .253 37240 240 49 47 8 236 116 32 7 54 12 35 265 176 223 .345 .84 0 .345
17 3.248 36708 50 11 48 9 50 44 33 13 78 32 37 56 1 18 3.324 .98 0 3.324
18 .585 36176 50 10 46 8 39 11 33 12 77 32 37 43 3 6 .812 .95 0 .812
19 -4.211 35644 138 21 45 9 38 12 33 7 52 12 37 42 82 5 -3.886 .21 0 -3.886
20 0 35112 52 13 49 10 36 7 33 8 76 32 37 40 2 3 .202 .94 0 .202

Total number of rows: 45220

Table truncated, full table size 3238 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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