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Sample GSM1070168 Query DataSets for GSM1070168
Status Public on Aug 31, 2013
Title UMA07122
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 Agilent protocol
 
Channel 2
Source name Reduction Mammoplasty Tissue
Organism Homo sapiens
Characteristics age: 19 years old
status: premenopausal
tissue: normal breast tissue
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Mini
Label Cy5
Label protocol Agilent standard protocol
 
 
Hybridization protocol Agilent standard protocol
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 Human breast tissue sample gene expression analyzed on agilent catalog 4X44k v1 human array
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Jan 24, 2013
Last update date Aug 31, 2013
Contact name Melissa Troester
E-mail(s) troester@unc.edu
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)
GSE43973 Age-associated gene expression in normal breast tissue mirrors qualitative age-at-incidence patterns for 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 1.083 1 2140 185 15 5 6482 981 33 13 1394 122 33 6482 2543 5387 1.602 .71 0
2 -1.5 2 26 8 15 5 35 13 32 12 1004 118 32 35 10 3 -1.737 -1 0
3 -1.119 3 25 7 15 5 36 14 33 13 1024 124 33 36 9 4 -1.737 -1 0
4 -1.252 4 27 10 14 4 39 14 34 12 970 128 34 39 12 5 -1.262 -1 0
5 -.999 5 26 10 14 5 40 16 35 12 1006 122 35 40 11 5 -1.136 -1 0
6 -.743 6 27 9 14 5 41 14 34 12 1006 124 34 41 13 7 -.778 .19 0
7 -.184 7 25 9 15 5 41 14 33 13 1052 128 33 41 10 9 -.322 -1 0
8 -.582 8 27 10 14 5 42 16 34 13 1044 128 34 42 13 8 -.584 -1 0
9 -2.581 9 27 7 14 5 37 17 36 13 1034 110 36 37 11 1 -3.591 -1 0
10 -2.316 10 26 10 14 5 37 10 36 13 1044 110 36 37 10 2 -3.458 -1 0
11 -.387 11 27 8 15 5 43 17 34 13 1016 116 34 43 12 9 -.29 .4 0
12 -3.391 12 500 74 14 5 100 33 36 13 990 124 36 100 572 54 -2.921 .53 0
13 -.989 13 49 15 14 5 55 19 35 13 1026 120 35 55 37 19 -.766 .19 0
14 .403 14 836 156 14 5 1565 379 36 13 1018 124 36 1565 975 1289 .899 .72 0
15 -.893 15 52 17 15 5 60 20 37 14 1048 134 37 60 40 21 -.685 .24 0
16 -1.208 16 8642 1381 15 5 5255 1249 35 12 1036 124 35 5255 10200 4415 -.725 .71 0
17 -2.32 17 97 27 15 5 55 20 35 12 986 128 35 55 91 18 -2.035 .38 0
18 -.731 18 51 14 15 5 59 22 34 12 988 130 34 59 39 23 -.527 -1 0
19 .137 19 54515 4922 15 5 72915 10443 35 13 978 110 35 72915 60099 66090 .419 .69 0
20 -.628 20 31 9 15 5 45 15 35 13 1018 130 35 45 16 10 -.584 -1 0

Total number of rows: 45220

Table truncated, full table size 3320 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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