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Sample GSM1523203 Query DataSets for GSM1523203
Status Public on Jun 22, 2015
Title Balbc_p53null_T11_sorted_miR200_plusDox1
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_plusDox1
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 -.02 1 38745 6429 19 13 24127 2880 39 27 10658 78 102 63492 30753 30333 .711 .5 0
2 .7 2 86 41 19 13 84 39 39 27 8670 88 102 221 43 70 .85 -1 0
3 .081 3 104 33 19 12 77 36 39 27 7326 76 102 202 55 58 .251 -1 0
4 .225 4 89 25 19 13 71 25 39 27 7186 82 102 186 44 51 .283 .52 0
5 .258 5 94 27 19 12 74 33 37 27 7244 88 97 194 48 58 .391 -1 0
6 .063 6 94 33 19 13 68 28 38 27 7304 92 98 178 47 49 .112 -1 0
7 .256 7 101 33 19 12 79 35 37 27 7244 84 97 207 54 64 .423 .41 0
8 .483 8 88 32 19 12 77 33 38 27 7344 86 100 202 44 62 .585 .6 0
9 .17 9 101 34 19 12 77 30 38 27 7180 86 100 202 53 60 .315 .36 0
10 .278 10 92 39 19 13 74 34 38 27 7260 86 100 194 47 57 .385 .52 0
11 .465 11 88 38 19 13 77 41 38 27 7216 86 100 202 44 61 .585 .35 0
12 .309 12 85 35 19 12 70 33 39 27 7196 86 102 184 41 51 .336 .39 0
13 .266 13 86 26 19 12 71 33 39 27 7262 86 102 186 42 51 .327 -1 0
14 .199 14 88 29 19 12 70 34 39 27 7266 86 102 184 43 50 .27 -1 0
15 .172 15 86 30 19 12 67 33 39 27 7202 82 102 176 41 46 .165 .33 0
16 .138 16 105 34 19 12 79 33 39 27 7314 88 102 207 56 62 .288 .38 0
17 .176 17 100 41 19 12 77 34 39 28 7282 86 102 202 52 59 .322 .32 0
18 .179 18 96 43 19 13 75 33 39 28 7262 92 102 197 49 56 .322 -1 0
19 .587 19 77 31 19 12 72 31 39 28 7302 84 102 189 35 53 .61 .33 0
20 -.062 20 85 32 19 13 61 26 39 28 7244 80 102 160 39 37 -.165 -1 0

Total number of rows: 180880

Table truncated, full table size 13587 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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