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Sample GSM1194987 Query DataSets for GSM1194987
Status Public on Oct 21, 2013
Title NCI10075
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, 38:121-141
 
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;Stromal proportion_tertile1;Epithelial proportion_tertile2;Adipose proportion_tertile3
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Mini
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-146
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-146
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 1.708 1 55063 3509 31 13 70671 7502 33 12 1372 112 31 67952 34490 112711 .303 .67 0
2 0 2 32 14 34 14 37 13 33 12 1032 120 31 35 0 0 0 .35 0
3 0 3 30 10 35 13 34 13 34 13 1056 122 32 32 0 0 0 .22 0
4 0 4 30 13 33 13 36 15 34 13 960 122 32 34 0 0 0 .4 0
5 -.322 5 34 17 33 13 37 16 35 12 976 134 33 35 2 1 0 .11 0
6 0 6 30 14 33 14 37 13 34 13 1046 124 32 35 0 0 0 .4 0
7 1.522 7 33 14 33 13 38 15 35 13 952 132 33 36 0 2 0 -1 0
8 0 8 32 16 34 12 42 14 34 12 970 122 32 40 0 0 0 -1 0
9 0 9 32 12 33 13 33 13 34 13 988 120 32 31 0 0 0 -1 0
10 0 10 32 10 34 13 37 14 35 13 1054 120 33 35 0 0 0 .1 0
11 -2.194 11 39 18 33 14 37 11 35 13 1010 124 33 35 8 1 -1.322 .43 0
12 -3.036 12 1414 286 33 14 114 37 34 13 994 124 32 109 952 116 -4.158 .59 0
13 -.424 13 41 19 32 12 42 15 35 13 1000 120 33 40 9 7 -.193 .36 0
14 .651 14 312 75 33 13 249 73 35 13 1010 128 33 239 195 307 -.432 .62 0
15 -.098 15 120 32 33 13 83 28 34 14 1000 118 32 79 68 63 -.87 -1 0
16 -1.416 16 10682 1711 33 13 1560 463 34 12 968 122 32 1500 6586 2467 -2.857 .64 0
17 -.141 17 86 22 32 12 67 26 35 13 1024 114 33 64 44 40 -.773 .2 0
18 -1.18 18 482 91 34 13 134 56 36 13 1000 136 34 128 317 140 -2.252 -1 0
19 .222 19 76441 10358 35 14 34874 8033 36 14 1032 118 34 33532 47769 55723 -1.191 .81 0
20 -1.618 20 46 16 34 14 40 17 36 13 1048 126 34 38 13 4 -1.322 -1 0

Total number of rows: 45220

Table truncated, full table size 3368 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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