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Sample GSM911195 Query DataSets for GSM911195
Status Public on Jan 18, 2013
Title Liu-30C Set1 vs. SCR1 Repl1
Sample type RNA
 
Channel 1
Source name MDA-MB231 scrambled
Organism Homo sapiens
Characteristics tissue type: breast cancer
cell line: MDA-MB231
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-127
 
Channel 2
Source name 30c MDA-MB231
Organism Homo sapiens
Characteristics tissue type: breast cancer
cell line: MDA-MB231
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-127
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-127
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Apr 09, 2012
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)
GSE32617 MicroRNA-30c inhibits Human Breast Tumor Chemotherapy Resistance by regulating TWF1 and IL-11: MDA-MB231 DataSet

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 -1.554 1 10151 990 61 13 3922 295 37 9 68 12 38 4085 10726 3654 -1.318 .99 0
2 -1.477 2 8994 2097 58 13 3627 577 41 9 27 12 42 3778 9445 3392 -1.258 .99 0
3 -.496 3 65 16 58 13 41 7 37 10 57 32 38 42 6 4 -.808 .99 0
4 -.721 4 65 15 61 12 41 9 39 12 49 32 40 42 3 2 -1 -1 0
5 -2.721 5 65 14 57 13 39 9 38 11 48 32 39 40 7 1 -3 .11 0
6 0 6 62 15 55 13 41 9 42 10 61 32 43 42 0 0 0 .08 0
7 -2.091 7 72 18 56 10 43 12 40 7 22 12 41 44 14 3 -2.411 .03 0
8 -1.424 8 65 13 55 11 41 9 38 9 53 32 39 42 8 3 -1.737 -1 0
9 -2.532 9 65 16 58 14 40 9 39 8 49 32 40 41 6 1 -2.806 .03 0
10 -.277 10 65 13 59 14 40 10 36 7 49 32 37 41 5 4 -.584 .14 0
11 -1.037 11 66 14 61 13 39 9 37 8 42 32 38 40 4 2 -1.322 .05 0
12 1.607 12 64 13 62 12 42 10 37 10 58 32 38 43 1 5 1.322 -1 0
13 .857 13 61 12 59 11 40 8 37 9 49 32 38 41 1 3 .585 .04 0
14 -1.137 14 67 13 56 9 41 11 37 13 48 32 38 42 9 4 -1.458 .21 0
15 -1.33 15 63 15 60 13 38 8 37 10 49 32 38 39 2 1 -1.586 .07 0
16 -.918 16 66 16 59 11 39 8 36 5 49 32 37 40 6 3 -1.221 .05 0
17 2.589 17 63 14 62 15 42 10 37 7 48 32 38 43 0 5 2.322 .14 0
18 0 18 69 14 60 13 39 7 40 11 49 32 41 40 0 0 0 .17 0
19 -1.738 19 65 14 61 14 40 8 39 9 58 32 40 41 3 1 -2 .03 0
20 .41 20 114 20 61 18 87 23 39 10 29 12 40 90 43 58 -.085 .65 0

Total number of rows: 45220

Table truncated, full table size 3020 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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