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Sample GSM571028 Query DataSets for GSM571028
Status Public on Jan 22, 2011
Title BALB_C4-HD2_1_LANARI
Sample type RNA
 
Channel 1
Source name Mouse Reference
Organism Mus musculus
Characteristics strain: BALB/c
tissue: whole mouse total RNA
Biomaterial provider Cam Patterson-UNC-CH
Extracted molecule total RNA
Extraction protocol Total RNA isolated by TRIZOL reagent
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
Channel 2
Source name BALB_C4-HD2_1_LANARI
Organism Mus musculus
Characteristics strain: BALB/c
tissue: mammary tumor
Biomaterial provider Claudia Lanari - Instituto de Biología y Medicina Experimental , Argentina
Treatment protocol MPA treatment
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 GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software.
Description BALB_C4-HD2_1_LANARI
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Jul 27, 2010
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 GPL10732
Series (1)
GSE23214 MPA-induced gene expression and stromal and parenchymal gene expression profiles in luminal murine mammary tumors with different hormonal requirements

Data table header descriptions
ID_REF Spot Reference ID
VALUE same as UNF_VALUE but with flagged values removed
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
UNF_VALUE log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN)

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 UNF_VALUE
1 .243 22575 93 34 53 27 80 45 59 37 521 156 60 82 26 31 -.862 .03 0 .243
2 -.721 22470 111 157 53 19 76 46 60 40 544 156 61 78 39 23 -1.771 .17 0 -.721
3 .189 22365 112 48 51 19 95 53 58 36 568 156 59 97 44 50 -.683 .3 0 .189
4 .199 22260 93 35 52 19 79 44 58 33 568 156 59 81 27 31 -.897 .11 0 .199
5 -1.012 22155 1348 804 54 19 801 509 58 39 544 156 59 825 1392 690 -.756 .94 0 -1.012
6 -1.283 22050 346 170 53 17 155 91 57 38 544 156 58 159 264 108 -1.535 .63 0 -1.283
7 .751 21945 93 55 53 17 89 140 56 38 544 156 57 91 28 47 -.234 .41 0 .751
8 -.049 21840 231 118 53 18 194 111 58 40 544 156 59 200 158 152 -.336 .69 0 -.049
9 .482 21735 92 33 55 18 82 49 59 40 568 156 60 84 24 34 -.624 .06 0 .482
10 -.18 21630 112 42 55 18 83 50 58 39 568 156 59 85 40 35 -1.133 .15 0 -.18
11 -.398 21525 182 84 52 18 121 62 57 38 544 156 58 124 104 79 -.977 .45 0 -.398
12 -.497 21420 128 48 53 18 86 51 58 40 544 156 59 88 54 38 -1.37 .17 0 -.497
13 .141 21315 173 81 53 17 150 100 60 39 544 156 61 154 98 109 -.368 .55 0 .141
14 -.404 21210 94 35 54 17 70 42 59 40 544 156 60 72 24 18 -1.737 .03 0 -.404
15 -.077 21105 216 121 54 18 175 109 59 41 568 156 60 180 140 133 -.432 .66 0 -.077
16 .081 21000 98 40 53 17 82 42 60 39 568 156 61 84 30 32 -.969 .09 0 .081
17 .207 20895 172 89 53 17 151 83 57 38 544 156 58 155 98 113 -.295 .6 0 .207
18 -1.097 20790 1584 880 53 18 905 532 57 41 544 156 58 932 1666 779 -.808 .93 0 -1.097
19 -.258 20685 3654 2484 53 19 4405 2962 62 40 544 156 63 4541 4324 3616 .315 .93 0 -.258
20 1.142 20580 365 183 55 19 775 452 62 39 544 156 63 798 316 698 1.245 .9 0 1.142

Total number of rows: 22575

Table truncated, full table size 1846 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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