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Sample GSM1166188 Query DataSets for GSM1166188
Status Public on Jan 21, 2015
Title 2250L cell line treated with 8Gy 8hr time point vs 0hr
Sample type RNA
 
Channel 1
Source name 2250L cell line 0hr
Organism Mus musculus
Characteristics cell line: 2250L
cell type: p53 null breast cancer
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-130
 
Channel 2
Source name 2250L cell line treated with 8Gy 8hr time point
Organism Mus musculus
Characteristics cell line: 2250L
cell type: p53 null breast cancer
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-130
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-135
Scan protocol Agilent Technologies Scanner Using Feature Extraction Software
Description 2250L cell line treated with 8Gy 8hr time point vs 0hr
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Jun 17, 2013
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)
GSE48073 Radiation induced gene signature predicts pathologic complete response to neoadjuvant chemotherapy in breast cancer patients

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 -.063 1 17958 716 30 15 21166 1819 40 20 10604 82 62 33071 19891 19041 .88 .24 0
2 -.969 2 50 22 31 16 44 19 39 20 8652 88 60 68 13 7 -1.086 .4 0
3 -.268 3 48 20 31 16 47 20 39 20 7422 82 60 73 13 10 -.106 -1 0
4 .288 4 45 24 32 16 47 23 39 20 7350 90 60 73 9 11 .241 -1 0
5 .791 5 47 22 33 16 54 23 39 20 7422 86 60 84 11 19 1 -1 0
6 -.946 6 44 15 33 16 40 21 39 20 7602 86 60 62 5 2 -2.171 -1 0
7 .25 7 51 24 33 16 53 26 39 20 7396 86 60 82 14 17 .459 -1 0
8 -1.83 8 56 20 33 16 41 20 39 20 7426 80 60 64 14 4 -2.396 -1 0
9 -.137 9 51 21 33 16 49 20 39 20 7456 82 60 76 14 13 0 .35 0
10 -.117 10 46 22 33 16 43 24 38 20 7422 90 59 67 9 8 -.584 -1 0
11 -.045 11 48 22 33 16 45 22 38 20 7166 82 59 70 10 10 -.241 .4 0
12 -.104 12 50 23 32 16 49 22 39 20 7138 84 60 76 14 13 0 .33 0
13 .544 13 44 18 32 16 48 24 39 20 7198 80 60 75 8 12 .585 .19 0
14 .852 14 42 19 32 16 46 21 38 20 7096 78 59 71 7 12 .585 -1 0
15 .72 15 42 18 32 16 47 23 39 20 7162 82 60 73 7 12 .7 -1 0
16 1.385 16 40 19 32 16 49 22 38 20 7052 82 59 76 6 16 1.28 -1 0
17 -.358 17 48 17 32 15 44 23 38 20 7200 84 59 68 11 9 -.637 -1 0
18 -1.313 18 51 23 32 15 42 17 39 20 7196 80 60 65 12 4 -1.766 .67 0
19 -.968 19 46 21 32 15 41 18 39 20 7214 92 60 64 7 4 -1.586 -1 0
20 .169 20 46 19 32 16 49 21 40 20 7260 86 62 76 10 12 .107 .16 0

Total number of rows: 180880

Table truncated, full table size 13011 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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