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Sample GSM1589827 Query DataSets for GSM1589827
Status Public on Mar 21, 2016
Title Strain_adenosquamous_partial-EMT_dox-treated_D723_UC-Denver
Sample type RNA
 
Channel 1
Source name Mouse Reference
Organism Mus musculus
Characteristics reference: Whole mouse total RNA
Biomaterial provider Perou Lab-UNC-CH
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
Channel 2
Source name FVB_Six1_Transgenic_D723
Organism Mus musculus
Characteristics sample: Mouse Transgenic Tumor
Biomaterial provider Perou Lab-UNC-CH
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 Agilent fluorescent scanner and image intensity data were extracted and analyzed with Agilent analysis software.
Description Mouse Transgenic Tumor
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Jan 22, 2015
Last update date Mar 21, 2016
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)
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
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 .146 1 11240 410 20 5 8695 346 42 16 10706 82 29 6038 9367 10366 -.9 .4 0
2 .628 2 23 5 21 6 48 17 42 16 8718 88 29 33 2 4 1 -1 0
3 1.353 3 22 6 21 6 49 19 43 16 7384 76 29 34 1 4 0 .29 0
4 0 4 18 6 21 6 43 20 43 16 7422 86 29 29 0 0 0 -1 0
5 -1.948 5 22 5 21 6 44 17 43 16 7224 86 29 30 2 0 0 .25 0
6 0 6 19 5 21 6 46 19 43 16 7312 88 29 31 0 0 0 -1 0
7 0 7 20 6 21 6 45 13 43 16 7322 84 29 31 0 0 0 .09 0
8 0 8 19 5 21 6 46 17 42 16 7272 88 29 31 0 0 0 -1 0
9 4.26 9 21 6 21 6 52 20 42 16 7230 92 29 36 0 5 0 .43 0
10 0 10 20 5 21 6 46 16 42 16 7342 80 29 31 0 0 0 -1 0
11 0 11 20 4 21 6 46 20 42 16 7272 76 29 31 0 0 0 -1 0
12 0 12 19 6 21 6 52 20 42 16 7190 86 29 36 0 0 0 .34 0
13 0 13 18 4 21 6 40 10 42 16 7294 80 29 27 0 0 0 .5 0
14 0 14 20 7 21 6 45 16 42 16 7186 86 29 31 0 0 0 .42 0
15 -1.479 15 21 7 21 6 43 18 43 16 7192 88 29 29 0 0 0 .57 0
16 .984 16 22 7 21 6 49 18 42 16 7376 78 29 34 2 5 2.322 -1 0
17 1.342 17 22 5 21 6 49 20 42 16 7352 74 29 34 1 4 2.322 -1 0
18 0 18 20 5 21 6 46 19 43 17 7434 78 29 31 0 0 0 .62 0
19 -.302 19 23 7 20 6 48 23 43 17 7392 80 29 33 4 3 1 .6 0
20 -.876 20 23 6 21 6 46 16 43 17 7366 88 29 31 3 2 0 .52 0

Total number of rows: 180880

Table truncated, full table size 12567 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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