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Sample GSM804364 Query DataSets for GSM804364
Status Public on Jan 31, 2021
Title STRAIN_MMTV_Neu_4T2_GRUBBS
Sample type RNA
 
Channel 1
Source name Whole Mouse Reference RNA-2009
Organism Mus musculus
Characteristics reference: Whole Mouse Reference
Biomaterial provider produced at UNC
Treatment protocol described in He et al., 2004. BioTechniques, Vol. 37:464-468
Growth protocol described in He et al., 2004. BioTechniques, Vol. 37:464-468
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
Channel 2
Source name Untreated MMTV-Neu+/- tumor RNA
Organism Mus musculus
Characteristics tumor: Mouse tumor derived RNA
genotype/variation: MMTV-Neu+/-
Biomaterial provider Clinton Grubbs and Ron Lubet University of Alabama
Treatment protocol described in Hu et al., 2005, BioTechniques, 38:121-124
Growth protocol described in Hu et al., 2005, BioTechniques, 38:121-124
Extracted molecule total RNA
Extraction protocol total RNA
Label Qiagen Rneasy Kit
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 Agilent Technologies Scanner G2505C US82800149 Using Feature Extraction Software
Description Untreated MMTV-Neu+/- tumor RNA versus whole mouse reference RNA
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Sep 29, 2011
Last update date Jan 31, 2021
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 GPL2881
Series (1)
GSE35188 DIMETHYLBENZANTHRACENE (DMBA) INDUCED MAMMARY CARCINOGENESIS IN MMTV-Neu and MMTV/p53 KO FEMALE MICE AND EFFECTS OF REXINOIDS

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 -8.349 22575 7880 4944 145 50 66 35 45 29 521 156 54 80 7276 22 -8.381 .21 0
2 -.984 22470 223 71 142 42 61 34 45 27 544 156 54 74 50 25 -2.017 .09 0
3 1.028 22365 250 84 140 44 177 112 44 29 568 156 53 215 84 172 .559 .64 0
4 -.631 22260 227 70 141 44 67 40 44 37 568 156 53 81 55 35 -1.617 .27 0
5 -.981 22155 2895 1708 139 42 1708 1033 43 30 544 156 52 2082 3009 1524 -.44 .98 0
6 -3.064 22050 735 348 140 44 93 59 45 30 544 156 54 113 488 58 -3.336 .43 0
7 1.485 21945 149 53 145 76 56 33 44 27 544 156 53 68 4 11 1.907 .46 0
8 -1.965 21840 613 317 142 76 133 84 46 28 544 156 56 162 399 102 -2.152 .68 0
9 -1.064 21735 223 74 142 43 61 35 46 28 568 156 56 74 50 24 -2.171 .1 0
10 -.317 21630 265 84 141 71 95 56 45 28 568 156 54 115 87 70 -1.023 .41 0
11 .258 21525 358 152 140 73 232 138 44 29 544 156 53 282 185 221 .07 .76 0
12 -1.183 21420 280 104 139 44 74 43 45 28 544 156 54 90 96 42 -1.971 .24 0
13 .743 21315 302 119 139 44 231 148 45 25 544 156 54 281 134 225 .478 .75 0
14 -.425 21210 229 81 139 55 75 47 46 23 544 156 56 91 59 44 -1.362 .2 0
15 -.528 21105 598 278 138 41 320 183 47 25 568 156 57 390 425 295 -.466 .9 0
16 -.775 21000 214 71 136 42 65 35 47 28 568 156 57 79 49 28 -1.826 .18 0
17 -.071 20895 272 108 138 46 114 71 45 27 544 156 54 139 98 93 -.657 .57 0
18 -1.042 20790 2716 1541 142 53 1517 911 47 27 544 156 57 1850 2791 1355 -.521 .96 0
19 -.428 20685 7062 3975 140 44 7015 4057 46 30 544 156 56 8554 8054 5989 .296 .99 0
20 .054 20580 533 223 139 45 401 246 46 31 544 156 56 489 367 381 .136 .89 0

Total number of rows: 22575

Table truncated, full table size 1764 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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