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Sample GSM1195022 Query DataSets for GSM1195022
Status Public on Oct 21, 2013
Title NCI10235
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 Qiagen Rneasy Mini
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-188
 
Channel 2
Source name Normal Tissue Adjacent to Breast Tumor
Organism Homo sapiens
Characteristics mammographic density: <25%
mammographic dense area: <median (36.52cm2)
microenvironment subtype: Active
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Mini
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-193
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-193
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.
Description Normal Tissue Adjacent to Breast Tumor
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Jul 24, 2013
Last update date Oct 21, 2013
Contact name Melissa Troester
E-mail(s) [email protected]
Organization name University of North Carolina at Chapel Hill
Department Epidemiology
Street address 135 Dauer Drive, CB 7435
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platform ID GPL4133
Series (1)
GSE49175 Relationship of mammographic density and gene expression: analysis of normal breast tissue surrounding 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 1.588 1 41738 2750 30 13 89812 7716 35 13 1400 120 33 84728 35289 106109 1.022 .49 0
2 -2.048 2 313 61 30 13 78 27 34 13 1032 130 32 73 227 55 -2.776 -1 0
3 -2.271 3 288 56 31 13 67 26 34 13 1014 124 32 63 204 42 -3.035 .55 0
4 -1.994 4 284 49 33 14 73 27 33 13 1028 130 31 68 200 50 -2.747 .53 0
5 -2.096 5 273 45 33 12 68 22 33 12 1028 124 31 64 190 44 -2.857 .32 0
6 -2.079 6 260 47 32 12 65 21 32 12 1014 122 30 61 180 42 -2.868 .49 0
7 -2.057 7 253 49 31 13 67 18 34 13 1012 112 32 63 176 42 -2.826 .32 0
8 -2.501 8 238 52 32 13 57 22 35 13 1026 126 33 53 162 28 -3.351 .46 0
9 -2.119 9 231 51 32 14 62 19 34 13 1054 124 32 58 157 36 -2.932 .29 0
10 -1.965 10 211 41 31 12 62 17 34 13 1018 122 32 58 142 36 -2.776 .27 0
11 -2.288 11 214 43 33 14 59 21 36 14 990 128 33 55 143 29 -3.023 .32 0
12 -2.329 12 1146 166 31 13 191 51 36 14 996 120 33 180 934 185 -2.921 .64 0
13 -1.884 13 179 41 32 12 59 18 35 13 1030 120 33 55 116 31 -2.727 .46 0
14 .321 14 413 77 31 13 370 96 35 12 1008 124 33 349 320 400 -.271 .61 0
15 -1.338 15 255 66 31 13 91 27 34 13 1028 122 32 85 180 71 -2.071 .23 0
16 -.406 16 7757 1283 31 13 3655 713 32 13 968 124 30 3448 6090 4596 -1.178 .79 0
17 -1.16 17 205 48 33 13 81 24 33 13 1020 126 31 76 137 61 -1.932 -1 0
18 -1.514 18 491 91 31 13 146 44 34 13 1008 126 32 137 384 134 -2.127 .38 0
19 .781 19 49511 7021 31 12 60448 11085 35 12 1028 114 33 57026 41706 71674 .204 .76 0
20 -1.672 20 160 40 31 12 59 25 34 12 1036 126 32 55 103 32 -2.49 .37 0

Total number of rows: 45220

Table truncated, full table size 3371 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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