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Sample GSM508508 Query DataSets for GSM508508
Status Public on May 27, 2011
Title Spain-263867
Sample type RNA
 
Channel 1
Source name Human Reference B
Organism Homo sapiens
Characteristics reference: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
Biomaterial provider Stratagene
Extracted molecule total RNA
Extraction protocol Total RNA isolated by stratagene
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
Channel 2
Source name Spain-263867
Organism Homo sapiens
Characteristics study: Madrid
age: 59
histologic grade (1=grade i (low); 2= grade ii (intermediate); 3= grade iii (high); 9 = n/a): 3
histology (1=necrosis; 2=ductal carcinoma; 3=lobular; 4=mixed ductal/lobular carcinoma; 5=other 6=no invasive tumor present; 9 = n/a ): 2
tumor size (pre-chemotherapy), cm (-1 = n/a): 5
tumor size (-1 = n/a; 1 = <= 2cm; 2 = 2-5 cm; 3 = > 5cm): 2
er (0=negative; 1=positive; 9 = n/a): 1
pgr (0=negative; 1=positive; 9 = n/a): 1
her2 (0=negative; 1=positive; 9 = n/a): 1
pam50 + claudin-low: Luminal B
neoadjuvant chemotherapy: Doxorubicin
number of positive nodes (post chemotherapy): 2
pcr: No
residual cancer burden index class: II
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 GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.
Description Spain-263867
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Feb 11, 2010
Last update date Jun 06, 2022
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 GPL7504
Series (1)
GSE21997 Genomic predictors of response to doxorubicin versus docetaxel in breast cancer
Relations
Reanalyzed by GSE205568

Data table header descriptions
ID_REF Spot Reference ID
VALUE same as UNF_VALUE but with flagged values removed
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
UNF_VALUE log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN)

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 UNF_VALUE
1 1.591 1 2561 2176 38 197 7392 5381 70 119 70 12 47 4994 2475 7461 .972 .79 0 1.591
2 1.156 2 2849 2002 35 221 6077 4404 51 134 55 32 34 4106 2758 6147 .533 .83 0 1.156
3 2.092 3 40 8 37 6 152 121 54 80 44 32 36 102 8 35 4.459 .94 0 2.092
4 .989 4 40 8 37 6 130 111 74 89 47 32 50 87 9 18 3.624 .1 0 .989
5 0 5 41 10 40 7 101 85 107 79 22 12 72 68 0 0 0 .14 0 0
6 -3.367 6 39 6 37 7 101 89 96 118 53 32 64 68 10 0 1 .04 0 -3.367
7 1.39 7 38 7 37 6 125 111 84 120 49 32 56 84 3 10 4.807 .05 0 1.39
8 .323 8 38 6 36 5 119 136 86 119 49 32 58 80 7 9 3.459 .08 0 .323
9 0 9 38 8 38 7 106 80 92 93 48 32 62 71 0 0 0 .03 0 0
10 -.519 10 41 7 38 7 95 94 69 95 46 32 46 64 10 7 2.585 .13 0 -.519
11 .88 11 40 6 37 6 122 90 69 82 53 32 46 82 9 17 3.585 .1 0 .88
12 -1.113 12 41 7 37 6 110 133 88 76 48 32 59 74 13 6 1.907 .07 0 -1.113
13 1.483 13 39 8 38 5 134 91 91 93 49 32 61 90 3 10 4.858 .17 0 1.483
14 1.058 14 41 8 39 6 144 127 96 100 49 32 64 97 6 14 4.044 .18 0 1.058
15 0 15 39 5 37 7 87 72 103 97 48 32 69 58 0 0 0 .1 0 0
16 .864 16 53 85 36 7 216 580 105 102 49 32 70 145 32 58 2.141 .96 0 .864
17 -.445 17 41 6 38 6 115 85 88 92 49 32 59 77 10 7 2.585 .03 0 -.445
18 -4.45 18 42 8 38 6 109 108 105 71 48 32 70 73 18 0 -.415 .2 0 -4.45
19 -1.025 19 41 6 37 6 103 125 80 85 55 32 54 69 13 6 1.907 .05 0 -1.025
20 .076 20 89 21 38 7 225 160 88 107 32 12 59 152 81 85 .867 .11 0 .076

Total number of rows: 45220

Table truncated, full table size 3208 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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