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Sample GSM823648 Query DataSets for GSM823648
Status Public on May 01, 2012
Title MCF10_H1047R_4Hr_vs_H1047R_0Hr_IL6R_Inhibitor_v1.0
Sample type RNA
 
Channel 1
Source name MCF10_H1047R_0Hr_IL6R_Inhibitor_v1.0
Organism Homo sapiens
Characteristics cell line: MCF-10A
genotype/variation: H1047R
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy3
Label protocol Agilent Quick Amp Labeling Kit
 
Channel 2
Source name MCF10_H1047R_4Hr_IL6R_Inhibitor_v1.0
Organism Homo sapiens
Characteristics cell line: MCF-10A
genotype/variation: H1047R
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy5
Label protocol Agilent Quick Amp Labeling Kit
 
 
Hybridization protocol described in Prat et al., 2010, Breast Cancer Research, 12:R68
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 v10.7.3.1
Description MCF-10A cells with the PIK3CA H1047R mutation were treated with an IL-6 receptor monoclonal antibody for 4 hours and compared to MCF-10A cells with the PIK3CA H1047R mutation.
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Oct 27, 2011
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 GPL10481
Series (1)
GSE33403 Oncogenic PI3K mutations lead to NF-kB-dependent cytokine expression following growth

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 -.478 1 40679 1924 16 8 42202 5153 37 14 1366 116 102 117227 48875 35080 1.527 -1 0
2 -.164 2 54 17 16 8 50 17 39 14 1006 128 108 138 22 20 -.302 .2 0
3 -.205 3 57 16 17 9 50 18 38 14 1020 134 105 138 24 21 -.241 -1 0
4 -.195 4 56 16 17 8 50 14 38 14 1020 134 105 138 23 20 -.204 .22 0
5 -.424 5 58 21 17 7 49 13 39 14 1026 126 108 136 23 17 -.55 .42 0
6 -.809 6 60 18 16 7 46 15 39 14 996 128 108 127 24 13 -1.178 .48 0
7 -.658 7 55 17 16 7 44 14 38 12 962 118 105 122 19 12 -1.123 .11 0
8 -.201 8 55 21 16 8 49 16 38 12 1008 130 105 136 22 19 -.255 -1 0
9 -.433 9 58 18 17 8 47 17 38 13 1024 130 105 130 23 17 -.642 .17 0
10 -.717 10 61 21 16 8 47 16 38 13 1018 132 105 130 26 15 -.816 .27 0
11 -.617 11 58 20 16 8 47 14 39 14 1032 122 108 130 22 14 -.862 .2 0
12 .183 12 237 47 16 7 304 80 38 13 998 112 105 844 227 258 1.748 -1 0
13 -.179 13 3919 659 17 8 4395 711 38 13 982 112 105 12208 4387 3876 1.634 .21 0
14 .004 14 699 137 16 8 837 214 37 14 1036 122 102 2325 738 740 1.707 .53 0
15 -.217 15 237 48 16 7 237 58 39 14 1006 122 108 658 226 194 1.322 -1 0
16 -.153 16 708 88 16 7 761 160 37 14 1004 108 102 2113 747 671 1.541 .52 0
17 -.241 17 65 22 16 8 58 22 38 14 998 126 105 161 34 29 .223 -1 0
18 .114 18 1477 249 16 8 1964 445 38 14 1016 120 105 5455 1612 1745 1.875 .73 0
19 -.41 19 173 45 16 8 151 41 38 14 984 134 105 419 153 115 1.019 .11 0
20 -.082 20 12981 2132 16 8 16430 2889 37 13 1002 114 102 45638 14998 14171 1.812 .7 0

Total number of rows: 45220

Table truncated, full table size 3460 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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