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Sample GSM1324868 Query DataSets for GSM1324868
Status Public on May 12, 2015
Title MDA-MB-436 ABT Carbo Study 251510210863_1
Sample type RNA
 
Channel 1
Source name Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
Organism Homo sapiens
Characteristics reference: Human Reference B
Biomaterial provider Stratagene
Growth protocol Total RNA isolated by stratagene
Extracted molecule total RNA
Extraction protocol Total RNA isolated by stratagene
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-504
 
Channel 2
Source name MDA-MB-436 ABT888 Mouse 282
Organism Homo sapiens
Characteristics cell line: MDA-MB-436
Treatment protocol ABT888
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-124
Scan protocol Agilent Technologies Scanner G2505C US82800149 Using Feature Extraction Software
Description MDA-MB-436 282 ABT 251510210863_1
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Feb 10, 2014
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)
GSE55399 Efficacy of carboplatin alone and in combination with ABT888 in intracranial murine models of BRCA-mutated and BRCA-wild-type triple negative breast cancer

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 1.509 1 65894 3909 24 11 98548 11943 38 14 1324 122 76 197096 47751 135889 1.581 .71 0
2 .432 2 38 13 26 11 46 14 38 13 978 120 76 92 8 11 .541 .21 0
3 -.958 3 41 17 26 11 43 16 39 13 978 114 78 86 11 5 -.701 .09 0
4 -.121 4 34 13 27 11 43 16 39 15 1016 120 78 86 5 5 .415 -1 0
5 -.695 5 37 12 27 11 42 13 38 14 1000 130 76 84 8 5 -.17 -1 0
6 -1.076 6 39 14 27 11 44 15 41 15 1032 126 82 88 9 4 -.876 -1 0
7 -1.426 7 38 12 27 11 42 16 40 14 1042 130 80 84 9 3 -1.171 .2 0
8 .083 8 40 16 27 11 45 17 38 14 1032 132 76 90 9 9 .348 .14 0
9 -.074 9 38 16 27 11 44 17 38 14 1042 128 76 88 8 8 .263 .37 0
10 -.45 10 37 15 27 12 42 17 38 14 1022 114 76 84 8 6 -.17 .27 0
11 -1.301 11 36 13 27 12 42 13 40 14 1036 120 80 84 7 3 -1 -1 0
12 1.54 12 59 24 26 12 67 25 40 13 1006 130 80 134 17 52 .801 -1 0
13 2.135 13 5954 707 28 11 8533 1574 40 13 980 126 79 17066 3385 14868 1.52 .27 0
14 -.834 14 509 103 29 11 100 34 40 14 1034 124 80 200 227 127 -2 .58 0
15 1.228 15 311 63 28 12 188 49 40 13 1002 122 80 376 134 314 .075 -1 0
16 -.131 16 498 85 28 12 135 36 39 14 982 128 78 270 222 203 -1.286 .54 0
17 -2.249 17 123 34 28 12 44 15 39 14 968 120 77 88 53 11 -3.095 -1 0
18 .989 18 449 114 28 11 228 64 38 13 1006 128 76 456 201 399 -.144 .66 0
19 1.202 19 125 37 29 12 88 25 38 12 984 130 76 176 45 105 .075 -1 0
20 -1.362 20 13401 2121 28 12 1631 285 39 15 980 120 78 3262 7400 2878 -2.071 .82 0

Total number of rows: 45220

Table truncated, full table size 3339 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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