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Sample GSM1214580 Query DataSets for GSM1214580
Status Public on Oct 29, 2013
Title HCC38 cell line
Sample type RNA
 
Channel 1
Source name Human Reference
Organism Homo sapiens
Characteristics references: Whole human total RNA
Biomaterial provider Perou Lab-UNC-CH
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-143
 
Channel 2
Source name HCC38 cell line
Organism Homo sapiens
Characteristics sample: Cell Line
Biomaterial provider Perou Lab-UNC-CH
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 Agilent fluorescent scanner and image intensity data were extracted and analyzed with Agilent analysis software.
Description 251510210423-4-4X44K
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Aug 22, 2013
Last update date Jul 17, 2015
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)
GSE50470 Characterization of Cell Lines Derived from Breast Cancers and Normal Mammary Tissues for the Study of the Intrinsic Molecular Subtypes

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 .243 1 1095 488 36 8 1431 438 35 17 67 12 34 1402 1117 1322 .37 .86 0
2 .29 2 1508 776 38 7 2077 502 36 14 30 12 35 2036 1566 1915 .445 .84 0
3 -.073 3 40 9 38 8 42 21 38 17 52 32 37 41 2 2 1 .95 0
4 0 4 36 9 36 9 42 18 45 25 49 32 44 41 0 0 0 .12 0
5 .324 5 38 9 35 9 47 24 40 24 49 32 39 46 4 5 1.222 .15 0
6 0 6 38 8 38 8 43 17 35 15 48 32 34 42 0 0 0 -1 0
7 -1.052 7 39 9 36 8 41 14 38 19 49 32 37 40 4 2 0 .07 0
8 -.866 8 39 9 34 9 44 20 39 22 49 32 38 43 6 3 0 .11 0
9 .585 9 38 8 36 7 41 17 35 16 48 32 34 40 2 4 1.585 .05 0
10 1.46 10 38 7 37 7 45 22 39 12 49 32 38 44 1 4 2.585 -1 0
11 -3.197 11 42 9 38 9 40 14 39 15 50 32 38 39 6 0 -2 .04 0
12 2.585 12 38 8 37 9 51 22 39 14 48 32 38 50 1 8 3.585 -1 0
13 .803 13 39 9 38 9 41 15 37 16 49 32 36 40 1 2 2 .08 0
14 0 14 37 8 38 8 44 21 35 17 49 32 34 43 0 0 0 .09 0
15 -.585 15 41 10 38 8 39 15 35 17 48 32 34 38 4 2 .415 .08 0
16 -.289 16 39 9 35 6 41 17 35 19 49 32 34 40 5 4 .585 .03 0
17 0 17 37 9 37 8 45 22 32 13 49 32 31 44 0 0 0 .13 0
18 .585 18 40 10 38 9 45 17 39 13 48 32 38 44 2 4 1.585 .23 0
19 -.586 19 40 9 36 8 41 13 36 16 49 32 35 40 5 3 .322 .13 0
20 .606 20 48 14 37 8 62 34 40 21 53 32 39 60 12 19 .933 .43 0

Total number of rows: 45220

Table truncated, full table size 2984 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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