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Sample GSM662248 Query DataSets for GSM662248
Status Public on Aug 15, 2011
Title FVB_MMTV_Neu_116916_PEROU
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 Cam Patterson - UNC
Extracted molecule total RNA
Extraction protocol Total RNA isolated by Trizol
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
Channel 2
Source name FVB_MMTV_Neu_116916_PEROU
Organism Mus musculus
Characteristics strain: FVB
tumor: mammary tumor
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Mini Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-579
Scan protocol scanned on Agilent scanner (model G2505B)
Description mammary tumor
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Jan 26, 2011
Last update date Jul 17, 2015
Contact name Charles M. Perou
E-mail(s) [email protected]
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)
GSE27101 Comparative oncogenomics identifies breast tumors enriched in functional tumor initiating cells
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)
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 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 .378 3221 151 173 39 7889 540 40 19 67 12 32 6362 4289 5576 1.055 .9 0
2 0 164 33 167 41 46 19 37 17 76 32 29 37 0 0 0 .71 0
3 -3.214 171 39 154 43 39 14 37 19 71 32 29 31 17 1 -3.083 .08 0
4 -1.207 167 40 150 41 42 19 35 13 71 32 28 33 16 7 -1.766 -1 0
5 0 163 34 165 38 44 16 40 16 72 32 32 35 0 0 0 .08 0
6 -1.527 180 40 162 35 45 17 39 17 71 32 31 36 17 6 -1.847 .05 0
7 -.759 172 36 160 31 48 19 41 14 71 32 33 38 11 7 -1.262 .08 0
8 0 177 40 157 31 39 12 39 14 72 32 31 31 0 0 0 .1 0
9 -.218 169 35 152 31 50 18 37 9 71 32 29 40 16 13 -.628 .03 0
10 1.885 167 35 166 35 42 12 37 16 71 32 29 33 1 4 2 .18 0
11 0 169 30 171 30 81 136 43 18 75 32 34 65 0 0 0 .98 0
12 1.459 180 38 168 39 65 30 37 18 76 32 29 52 11 30 .939 .13 0
13 -3.259 4048 364 168 33 735 99 41 14 51 12 33 592 5076 530 -2.796 .95 0
14 .246 334 62 169 35 126 54 39 19 36 12 31 101 110 130 -1.238 .69 0
15 1.521 180 38 167 35 70 35 39 18 78 32 31 56 11 34 .943 .77 0
16 1.252 320 42 167 32 324 90 43 15 53 12 34 261 134 319 .569 .78 0
17 0 161 36 169 34 52 21 44 18 80 32 35 41 0 0 0 .86 0
18 1.162 181 44 163 34 71 28 39 20 80 32 31 57 16 35 .53 .84 0
19 -.559 185 39 167 39 50 21 39 13 78 32 31 40 17 11 -1 .12 0
20 1.67 171 41 157 36 76 43 40 14 76 32 32 61 12 40 1.05 .46 0

Total number of rows: 45220

Table truncated, full table size 2822 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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