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Sample GSM1046951 Query DataSets for GSM1046951
Status Public on Nov 04, 2013
Title STAT1-/-_Schreiber_4524
Sample type RNA
 
Channel 1
Source name Whole Mouse Reference RNA
Organism Mus musculus
Characteristics reference: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups
Biomaterial provider Charles Perou - UNC
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen RNeasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
Channel 2
Source name STAT1-/-_Schreiber_4524
Organism Mus musculus
Characteristics sample: STAT1null
Biomaterial provider Robert Schreiber - Washington University
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-125
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software
Description Mammary Tumor
Data processing Data for both channels were Lowess-normalized and then the log(2) ratio was taken
 
Submission date Nov 29, 2012
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 (2)
GSE42640 Transcriptomic Classification of Genetically Engineered Mouse Models of Breast Carcinoma Identifies Human Subtype Counterparts
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 -1.365 1 11789 951 20 11 10912 1394 39 23 10690 74 34 9656 18154 7048 -.29 -1 0
2 .598 2 29 13 21 11 49 32 39 23 8762 86 34 43 7 11 .363 -1 0
3 -.759 3 34 13 21 12 44 23 38 23 7242 86 33 38 11 6 -1.136 -1 0
4 -.832 4 41 17 21 12 50 30 38 22 7256 82 33 44 21 12 -.711 .18 0
5 -.084 5 33 13 22 12 46 24 38 22 7180 80 33 40 10 9 -.515 -1 0
6 -.765 6 47 25 22 12 55 27 38 22 7332 84 33 48 27 16 -.617 .32 0
7 -.926 7 42 18 22 12 48 21 38 22 7216 86 33 42 20 10 -1 .22 0
8 -2.669 8 38 16 22 12 39 18 38 22 7138 90 33 34 11 1 -3.9 .4 0
9 0 9 45 19 22 12 36 21 37 23 7100 84 32 31 0 0 0 -1 0
10 -.253 10 36 16 22 12 48 23 37 23 7112 92 32 42 14 11 -.264 .3 0
11 .125 11 32 16 22 12 46 28 38 23 7156 84 33 40 9 9 -.193 .41 0
12 -1.665 12 44 17 21 12 44 23 38 23 7196 88 33 38 22 6 -2 -1 0
13 -1.42 13 41 19 22 12 44 25 38 23 7246 82 33 38 18 6 -1.847 -1 0
14 -1.559 14 39 20 21 12 42 24 38 23 7146 86 33 37 15 5 -1.905 .54 0
15 -.61 15 35 17 21 12 45 21 37 23 7166 84 32 39 13 8 -.778 .35 0
16 -1.214 16 35 19 21 12 41 22 37 23 7192 84 32 36 11 4 -1.458 -1 0
17 -.507 17 36 18 22 12 46 22 37 23 7148 82 32 40 14 9 -.701 .03 0
18 -.23 18 38 14 22 12 52 19 38 23 7214 78 33 46 16 14 -.206 .22 0
19 -.705 19 39 20 22 12 48 28 38 23 7204 92 33 42 17 10 -.831 -1 0
20 -.482 20 31 14 21 12 43 20 38 23 7232 76 33 38 8 6 -.678 .52 0

Total number of rows: 180880

Table truncated, full table size 13350 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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