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Sample GSM1166180 Query DataSets for GSM1166180
Status Public on Jan 21, 2015
Title 2225L-H cell line treated with 8Gy 48hr time point vs 0hr
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, 38:121-128
 
Channel 2
Source name 2225L cell line treated with 8Gy 48hr time point
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, 38:121-128
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-127
Scan protocol Agilent Technologies Scanner Using Feature Extraction Software
Description 2225L cell line treated with 8Gy 48hr time point vs 0 hr
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 .309 1 21515 1547 31 15 41951 2156 37 21 10616 82 31 35855 26959 33402 .738 -1 0
2 -1.561 2 65 28 33 16 51 24 38 21 8684 78 32 43 35 12 -1.446 .4 0
3 -1.449 3 52 22 34 17 44 21 38 21 7358 82 32 37 18 6 -1.68 .22 0
4 -.688 4 53 18 35 17 50 23 38 21 7402 90 32 42 19 12 -.766 .36 0
5 -1.65 5 60 22 35 16 47 27 39 20 7314 86 33 40 26 8 -1.718 -1 0
6 -.777 6 52 20 35 16 49 21 39 21 7354 76 33 41 17 10 -.908 -1 0
7 -2.016 7 59 25 35 17 45 22 39 21 7386 84 33 38 24 6 -2.139 -1 0
8 -1.225 8 54 23 34 16 47 20 38 21 7368 82 32 40 21 9 -1.171 .19 0
9 -1.499 9 59 25 34 16 48 20 39 21 7360 80 32 41 26 9 -1.355 -1 0
10 -1.662 10 58 22 34 16 46 21 38 21 7450 84 32 39 25 8 -1.653 -1 0
11 .279 11 46 20 34 16 53 21 38 21 7452 78 32 45 12 14 .379 -1 0
12 .66 12 46 13 34 16 58 26 38 20 7414 76 32 49 12 19 .918 -1 0
13 -.306 13 52 19 34 16 55 23 39 21 7404 84 33 47 19 15 -.1 .31 0
14 -1.234 14 59 22 34 16 51 23 39 21 7478 82 33 43 26 11 -1.136 -1 0
15 -1.876 15 62 24 34 16 47 19 39 21 7402 88 33 40 29 8 -1.894 .33 0
16 -1.27 16 59 26 34 16 51 26 39 21 7424 78 33 43 27 11 -1.201 .4 0
17 -.327 17 50 20 34 16 52 29 38 21 7490 86 32 44 17 14 -.223 .12 0
18 -.944 18 51 21 34 16 47 22 38 21 7262 78 32 40 17 9 -.908 -1 0
19 -.052 19 51 25 34 16 57 26 38 21 7222 84 32 48 18 17 .094 .41 0
20 -.972 20 60 29 33 16 56 24 39 21 7288 76 33 47 31 15 -.837 .18 0

Total number of rows: 180880

Table truncated, full table size 12974 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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