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Sample GSM714341 Query DataSets for GSM714341
Status Public on Dec 31, 2011
Title UNC971091A
Sample type RNA
 
Channel 1
Source name Human Reference B
Organism Homo sapiens
Characteristics sample type: reference
composition: Stratagene Human Universal Reference containing 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 (PMID: 15679094).
 
Channel 2
Source name Normal Tissue Adjacent to Breast Tumor
Organism Homo sapiens
Characteristics tissue: normal tissue adjacent to breast tumor
patient id: UNC971091
active or "inactive": positive
age at diagnosis (year): 51
menopause status: unknown
histopathology: Invasive
breast cancer subtype (pam50): unknown
er status: positive
hormone treated: no
her2 status: unknown
tumor grade: 1
tumor size (cm): 3.5
overall survival event (dead=1, alive=0): 0
overall survival (month): 21
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy Mini Kit.
Label Cy5
Label protocol Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).
 
 
Hybridization protocol Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).
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 Agilent Custom array of UNC971091A
Data processing Data for both channels were Lowess-normalized using the University of North Carolina (UNC) microarray database, and then the log(2) ratio (test/reference) was taken.
 
Submission date Apr 25, 2011
Last update date Dec 31, 2011
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 GPL10481
Series (1)
GSE31589 Expression of Epithelial-to-Mesenchymal Transition (EMT)-associated genes in extratumoral microenvironment predicts poor clinical outcome in breast cancer patients

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 1.778 1 9954 947 16 5 49624 4635 36 13 1400 110 22 31607 11988 41109 1.669 .68 0
2 -.793 2 21 6 16 6 39 15 37 13 1034 124 23 24 5 2 -2 -1 0
3 -.904 3 23 9 16 5 42 16 38 12 1030 128 24 26 8 4 -1.586 -1 0
4 -.516 4 22 5 16 5 41 14 37 14 1046 112 23 26 6 4 -.737 .59 0
5 -.285 5 23 7 16 5 45 15 37 14 1042 130 23 28 8 7 -.486 -1 0
6 -1.247 6 22 7 16 6 40 16 38 13 994 124 24 25 6 2 -2.322 .4 0
7 -.643 7 22 7 16 5 40 13 36 14 1002 116 22 25 6 4 -.737 .07 0
8 -.529 8 24 8 16 6 42 15 35 14 1030 124 22 26 9 6 -.808 .29 0
9 .313 9 21 8 16 5 44 15 37 13 1022 122 23 28 5 6 .322 -1 0
10 -.187 10 22 7 16 5 43 14 37 13 1046 132 23 27 6 5 -.322 .27 0
11 -1.152 11 23 7 16 5 40 12 37 12 1008 126 23 25 8 3 -1.806 -1 0
12 .334 12 82 21 16 5 179 55 35 12 1004 120 22 114 87 109 .501 .55 0
13 1.082 13 432 70 15 5 1383 179 37 13 1026 124 23 880 515 1091 1.043 -1 0
14 .236 14 706 133 16 5 1257 284 36 12 1002 124 22 800 846 996 .175 .66 0
15 1.29 15 194 57 16 5 740 138 36 12 1038 128 22 471 226 553 1.343 .32 0
16 -.471 16 563 84 15 4 651 128 36 13 990 120 22 414 684 493 -.48 .69 0
17 1.527 17 157 38 16 5 703 154 35 13 1040 116 22 447 181 522 1.592 .46 0
18 -.16 18 725 146 16 5 998 279 37 13 1008 122 23 635 873 781 -.213 .51 0
19 -.501 19 128 25 16 6 175 46 38 13 1022 108 24 111 147 104 -.351 .46 0
20 -.654 20 16080 3053 16 5 14445 2965 38 14 972 124 24 9200 19085 12126 -.808 .77 0

Total number of rows: 45220

Table truncated, full table size 3383 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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