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Sample GSM1368060 Query DataSets for GSM1368060
Status Public on Apr 17, 2014
Title 252550310118-1
Sample type RNA
 
Channel 1
Source name Whole Mouse Reference RNA-2009
Organism Mus musculus
Characteristics reference: Whole Mouse Reference
Biomaterial provider produced at UNC
Treatment protocol described in He et al., 2004. BioTechniques, Vol. 37:464–468
Growth protocol described in He et al., 2004. BioTechniques, Vol. 37:464–468
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-504
 
Channel 2
Source name Tumor RNA, Non-treated
Organism Mus musculus
Characteristics tumor: Mouse tumor derived RNA
Biomaterial provider Sean Egan PhD. University of Toronto. segan@sickkids.ca
Treatment protocol described in Hu et al., 2005, BioTechniques, 38:121-124
Growth protocol described in Hu et al., 2005, BioTechniques, 38:121-124
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 Agilent Technologies Scanner G2505C US82800149 Using Feature Extraction Software
Description Strain_MMTV-Cre_Lfng-flox/flox_3751_Egan
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Apr 11, 2014
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 GPL11383
Series (1)
GSE28712 Lunatic Fringe Deficiency Cooperates with the Met/Caveolin Gene Amplicon to Induce Basal-Like Breast Cancer

Data table header descriptions
ID_REF Spot Reference ID
VALUE log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN)
SPOT spot number on array
CH1_MEAN
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
LOG_RAT2N_MEAN log2_ratio of channel 2 normalized over channel 1 (global normalization)
CORR correlation coefficient among pixels
FLAG Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots

Data table
ID_REF VALUE 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 LOG_RAT2N_MEAN CORR FLAG
1 -.422 1 11225 871 18 11 7088 1055 37 19 10494 84 80 15408 10288 7681 .452 .43 0
2 .834 2 29 18 18 11 48 28 37 19 8622 90 80 104 8 15 1.415 .41 0
3 .411 3 26 12 19 11 41 25 37 20 7434 84 80 89 5 6 .585 .4 0
4 0 4 33 18 19 11 35 16 37 20 7332 84 80 76 0 0 0 -1 0
5 2.794 5 22 9 19 11 43 20 36 19 7276 84 78 93 1 12 3.907 .32 0
6 1.613 6 24 14 19 11 44 20 37 19 7280 90 80 95 3 10 2.322 -1 0
7 1.517 7 24 12 19 11 43 23 37 19 7218 88 80 93 3 9 2.115 .15 0
8 1.212 8 26 13 19 11 46 20 37 19 7436 82 80 100 5 12 2 .47 0
9 -.462 9 32 16 19 11 42 22 37 20 7426 86 80 91 9 7 0 .17 0
10 1.048 10 24 11 18 11 42 13 37 20 7250 70 80 91 3 8 1.875 .24 0
11 0 11 28 15 19 11 36 18 37 19 7284 78 80 78 0 0 0 .35 0
12 1.285 12 26 16 18 11 46 25 36 19 7448 90 78 100 5 14 2.138 .36 0
13 1.773 13 24 13 19 11 46 23 36 19 7292 88 78 100 4 14 2.874 .25 0
14 1.469 14 25 13 19 11 45 24 36 19 7404 82 78 97 4 12 2.248 -1 0
15 -.114 15 27 16 19 11 39 22 36 19 7344 92 78 84 5 5 0 .17 0
16 2.32 16 23 12 19 11 45 16 36 19 7370 90 78 97 2 14 3.248 -1 0
17 1.11 17 25 16 19 11 43 19 37 20 7394 86 80 93 4 9 1.7 -1 0
18 -.17 18 28 15 19 11 40 20 37 20 7316 82 80 86 5 5 -.223 -1 0
19 1.411 19 25 12 19 11 46 24 37 20 7264 82 80 100 4 12 2.322 .46 0
20 1.759 20 24 14 19 11 45 23 37 20 7264 82 80 97 3 12 2.503 .41 0

Total number of rows: 180880

Table truncated, full table size 12992 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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