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Sample GSM1166179 Query DataSets for GSM1166179
Status Public on Jan 21, 2015
Title 2225L-H cell line treated with 8Gy 24hr time point vs 0hr #2
Sample type RNA
 
Channel 1
Source name 2225L cell line 0hr
Organism Mus musculus
Characteristics cell line: 2225L-H
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, 38:121-127
 
Channel 2
Source name 2225L cell line treated with 8Gy 24hr time point #2
Organism Mus musculus
Characteristics cell line: 2225L-H
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, 38:121-127
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-126
Scan protocol Agilent Technologies Scanner Using Feature Extraction Software
Description 2225L cell line treated with 8Gy 24hr time point #2 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 .584 1 20439 818 27 14 50552 2553 36 20 10504 80 37 52115 26231 39310 1.352 .49 0
2 -.957 2 57 25 28 14 53 25 37 21 8626 94 38 54 30 15 -.701 .21 0
3 -1.313 3 53 25 30 15 46 21 38 20 7154 82 39 47 22 9 -1.392 -1 0
4 -1.017 4 56 21 31 15 49 26 37 20 7246 82 38 50 25 12 -.938 .26 0
5 -1.275 5 58 21 31 15 48 30 38 20 7158 90 39 49 26 10 -1.322 -1 0
6 -.236 6 50 21 31 15 53 26 38 20 7158 84 39 54 18 15 -.181 .32 0
7 -.363 7 50 21 31 15 52 23 37 20 7328 84 38 53 19 15 -.264 .19 0
8 -1.691 8 57 19 31 15 44 21 37 20 7380 80 38 45 24 7 -1.776 -1 0
9 -1.689 9 60 22 31 15 45 20 37 20 7328 88 38 46 28 8 -1.756 .15 0
10 -1.13 10 62 27 31 15 52 26 37 20 7342 90 38 53 32 14 -.952 .06 0
11 -1.035 11 57 24 31 15 50 25 37 20 7212 88 38 51 26 13 -.943 .32 0
12 -.351 12 50 15 31 15 50 29 36 20 7164 78 37 51 18 14 -.279 .41 0
13 -2.264 13 58 24 30 15 40 19 36 20 7304 84 37 41 26 5 -2.699 -1 0
14 -.692 14 49 20 30 15 47 19 37 20 7262 86 38 48 18 11 -.766 .4 0
15 -1.853 15 64 26 30 15 46 22 37 20 7292 84 38 47 34 9 -1.831 .32 0
16 -1.598 16 55 23 30 15 44 23 37 20 7174 80 38 45 24 8 -1.776 .57 0
17 -1.521 17 56 25 30 15 45 23 37 20 7066 84 38 46 25 8 -1.586 -1 0
18 -1.084 18 53 25 30 15 46 18 37 20 7188 82 38 47 21 10 -1.152 -1 0
19 -1.171 19 55 24 30 15 47 22 37 20 7280 86 38 48 24 10 -1.201 .19 0
20 -1.47 20 58 20 30 15 47 21 38 20 7178 82 39 48 27 10 -1.531 .42 0

Total number of rows: 180880

Table truncated, full table size 12989 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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