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Sample GSM381102 Query DataSets for GSM381102
Status Public on Jun 11, 2009
Title Agilent-8439_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-LPA2 transgenic mouse
Organism Mus musculus
Characteristics tissue: mammary tumor from MMTV-LPA2 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-LPA2 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 .93 45220 2723 312 60 16 5981 1109 45 68 397 80 38 5111 2907 5436 .903 .96 0 .903
2 4.644 44688 61 15 60 17 74 69 45 62 378 80 38 63 4 6 .646 .03 0 .646
3 0 44156 61 15 61 16 77 72 42 79 196 52 35 65 0 0 0 .03 0 0
4 0 43624 58 15 60 15 75 61 43 67 463 120 36 64 0 0 0 .05 0 0
5 2 43092 64 16 59 15 65 55 41 68 388 80 35 55 14 8 -.74 .03 0 -.74
6 3.524 42560 62 16 60 17 68 71 42 57 476 120 35 58 7 7 -.019 .06 0 -.019
7 3.17 42028 64 13 60 14 86 65 44 66 91 32 37 73 10 16 .691 .06 0 .691
8 3.907 41496 61 17 59 16 76 73 40 65 504 120 34 64 6 10 .723 .06 0 .723
9 5.644 40964 59 17 58 16 101 91 43 57 320 52 36 86 3 16 2.23 -1 0 2.23
10 3.954 40432 63 20 61 17 75 70 39 57 196 32 33 64 6 10 .723 .08 0 .723
11 4.644 39900 62 14 61 17 72 61 43 65 484 120 36 61 4 6 .646 -1 0 .646
12 2.459 39368 65 18 59 17 81 73 43 63 319 80 36 69 14 16 .217 .06 0 .217
13 -2.727 38836 2400 521 59 16 456 244 41 59 369 80 35 389 2338 415 -2.493 .81 0 -2.493
14 -2.252 38304 180 40 56 15 78 60 47 59 358 80 40 66 148 25 -2.526 .07 0 -2.526
15 1.524 37772 82 21 58 13 125 105 44 58 352 80 37 106 33 58 .821 .16 0 .821
16 .233 37240 177 43 57 16 207 164 41 66 307 80 35 176 118 168 .516 .5 0 .516
17 3.7 36708 60 16 58 16 72 62 42 62 437 120 35 61 6 8 .307 .03 0 .307
18 1.807 36176 64 18 58 16 64 54 39 59 468 120 33 54 15 9 -.743 .1 0 -.743
19 .53 35644 76 24 58 16 74 82 44 64 475 120 37 63 33 16 -1.063 .08 0 -1.063
20 2.485 35112 64 16 59 16 76 60 43 67 522 120 36 64 12 12 .006 -1 0 .006

Total number of rows: 45220

Table truncated, full table size 3574 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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