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Sample GSM1523205 Query DataSets for GSM1523205
Status Public on Jun 22, 2015
Title Balbc_p53null_T11_sorted_miR200_plusDox3
Sample type RNA
 
Channel 1
Source name Whole Mouse Reference RNA
Organism Mus musculus
Characteristics reference: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups
Biomaterial provider Charles Perou - UNC
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen RNeasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
Channel 2
Source name Balbc_p53null_T11_sorted_miR200c_plusDox3
Organism Mus musculus
Characteristics strain: Balbc
tissue: p53null mammary tumor
Biomaterial provider Jeffrey Rosen - Baylor
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen miRNeasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-125
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software
Description Passaged Mammary Tumor
Data processing Data for both channels were Lowess-normalized and then the log(2) ratio was taken
 
Submission date Oct 09, 2014
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 GPL11383
Series (1)
GSE62230 Expression of miR-200c in claudin-low breast cancer alters stem cell functionality, enhances chemosensitivity and reduces metastatic potential

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 -.501 1 35632 2312 18 12 15551 1799 38 25 10554 68 80 33087 27959 19761 -.109 .29 0
2 .304 2 100 40 18 12 84 33 38 25 8628 94 80 178 55 68 .293 .42 0
3 -.06 3 92 35 18 12 68 25 38 25 7262 84 80 144 48 46 -.17 .06 0
4 .257 4 94 34 18 12 78 18 38 25 7114 74 80 165 51 61 .2 .25 0
5 .226 5 93 31 18 11 76 42 38 25 7200 84 80 161 50 58 .131 .58 0
6 .369 6 90 33 18 11 79 33 38 25 7244 86 80 168 48 62 .309 .55 0
7 .595 7 83 28 18 11 81 40 37 25 7206 88 78 172 43 66 .555 .34 0
8 .18 8 98 30 18 12 77 33 37 25 7296 90 78 163 53 60 .124 .2 0
9 .232 9 91 34 18 12 76 34 38 25 7244 86 80 161 48 57 .17 -1 0
10 .41 10 83 23 18 12 75 32 38 25 7258 84 80 159 42 56 .327 -1 0
11 .431 11 77 27 18 12 71 32 38 26 7246 86 80 151 38 51 .317 -1 0
12 -.093 12 85 35 18 12 64 25 39 25 7262 78 82 136 42 40 -.29 .54 0
13 -.307 13 95 31 18 12 64 27 39 26 7292 82 82 136 49 40 -.474 .57 0
14 -.257 14 102 34 18 12 69 31 38 26 7294 84 80 146 56 46 -.331 .35 0
15 .113 15 92 35 18 12 73 36 38 26 7246 90 80 155 49 53 .059 -1 0
16 .243 16 86 26 18 12 73 35 38 26 7188 88 80 155 45 53 .162 -1 0
17 -.068 17 107 34 18 12 76 36 38 25 7162 84 80 161 60 57 -.12 -1 0
18 .666 18 83 32 18 12 84 37 38 25 7218 84 80 178 43 69 .638 .25 0
19 .304 19 81 31 18 12 71 31 38 25 7240 92 80 151 41 51 .195 .41 0
20 .135 20 89 31 18 12 71 38 38 25 7120 80 80 151 46 51 .02 .48 0

Total number of rows: 180880

Table truncated, full table size 13478 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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