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Sample GSM847925 Query DataSets for GSM847925
Status Public on Jun 25, 2013
Title 9830-000517B-244Kv5
Sample type RNA
 
Channel 1
Source name Human Reference
Organism Homo sapiens
Characteristics reference: Whole human total RNA
Biomaterial provider Perou Lab-UNC-CH
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
Channel 2
Source name 9830-000517B-244Kv5
Organism Homo sapiens
Characteristics tumor: Tumor sample
Biomaterial provider Perou Lab-UNC-CH
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 Fluorescent array images were collected for both Cy3 and Cy5 with a Agilent fluorescent scanner and image intensity data were extracted and analyzed with Agilent analysis software.
Description Tumor sample
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Dec 12, 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 GPL8269
Series (3)
GSE34412 A Renewable Tissue Resource of Phenotypically Stable, Biologically and Ethnically Diverse, Patient-derived Human Breast Cancer Xenografts
GSE41119 Molecular Characterization of Basal-like and Non-Basal-like Triple-Negative Breast Cancers
GSE46604 Xenografting of advanced stage breast cancer preserves the genomic and clonal architecture and captures luminal tumors harboring mutations and gene rearrangements in ESR1

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 1.003 1 15120 1466 14 6 50691 3821 40 14 1350 118 68 87398 19536 39166 2.532 .53 0
2 .32 2 36 13 14 5 61 16 40 14 1022 120 68 105 19 24 .75 .05 0
3 .556 3 33 10 13 5 61 17 39 14 1032 120 67 105 17 26 1 .17 0
4 -.01 4 965 153 13 5 1659 402 37 13 1020 126 63 2860 1247 1239 1.556 .82 0
5 0 5 1 1 1 1 1 0 0 1 2 2 0 1 0 0 0 1 0
6 .606 6 46 13 13 4 96 24 36 14 1012 114 62 165 36 55 1.642 .28 0
7 -.075 7 39 11 13 4 56 19 37 14 1034 122 63 96 23 22 .401 -1 0
8 .876 8 59 18 13 5 160 55 36 13 996 120 62 275 55 102 2.243 .36 0
9 .46 9 46 15 12 5 90 27 35 12 978 122 60 155 37 50 1.526 .06 0
10 .672 10 34 12 13 5 65 18 36 12 1026 124 62 112 20 32 1.252 -1 0
11 -.052 11 41 13 12 4 62 22 36 13 1002 128 62 106 28 27 .601 .32 0
12 .852 12 374 57 13 5 1169 158 37 12 1046 110 63 2015 476 860 2.435 .59 0
13 0 13 1 1 1 1 1 0 0 1 2 2 0 1 0 0 0 1 0
14 -.234 14 38 11 12 4 51 16 35 12 994 124 60 87 22 19 .111 -1 0
15 -.132 15 58 16 13 5 88 25 37 13 1022 118 63 151 50 45 1 .31 0
16 -.054 16 36 12 12 4 52 16 36 13 1004 122 62 89 20 19 .231 .28 0
17 -.879 17 808 157 12 5 785 165 36 12 1028 118 62 1353 1047 569 .7 .48 0
18 .394 18 38 13 13 5 66 25 36 12 1038 126 62 113 24 32 1.029 .31 0
19 -.021 19 36 11 12 5 54 15 36 13 1040 124 62 93 21 21 .431 .23 0
20 -.676 20 3977 566 12 5 4196 864 36 12 1018 112 62 7234 5133 3214 .855 .53 0

Total number of rows: 243504

Table truncated, full table size 18299 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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