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Sample GSM804359 Query DataSets for GSM804359
Status Public on Jan 31, 2021
Title STRAIN_MMTV_Neu_p53het_6T2_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+/- TP53+/- tumor RNA
Organism Mus musculus
Characteristics tumor: Mouse tumor derived RNA
genotype/variation: MMTV-Neu+/- TP53+/-
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+/- TP53+/- 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 -8.412 22575 7475 4352 56 21 86 42 62 46 521 156 59 82 7788 22 -8.381 .19 0
2 -.257 22470 125 50 57 19 75 44 58 42 544 156 55 72 37 31 -2 .06 0
3 .752 22365 186 85 59 19 225 134 57 39 568 156 54 216 112 189 .352 .74 0
4 -.05 22260 143 61 60 19 93 53 57 38 568 156 54 89 55 53 -1.245 .26 0
5 .331 22155 1443 787 58 20 2509 1494 56 40 544 156 53 2412 1643 2067 .768 .96 0
6 -3.342 22050 655 357 55 20 105 58 55 38 544 156 52 100 551 54 -3.644 .42 0
7 1.001 21945 60 19 55 20 67 40 53 36 544 156 50 64 5 11 1.485 .03 0
8 -1.006 21840 312 154 55 20 161 95 55 38 544 156 52 154 233 116 -1.333 .69 0
9 -.387 21735 123 51 54 19 73 38 58 39 568 156 55 70 36 28 -2.204 .06 0
10 -.18 21630 167 79 55 19 112 63 55 39 570 156 52 107 85 75 -1.026 .43 0
11 -.618 21525 405 196 57 20 284 165 58 39 544 156 55 273 347 226 -.676 .82 0
12 -.991 21420 192 82 59 21 95 57 60 38 544 156 57 91 96 48 -1.966 .32 0
13 .02 21315 301 139 58 19 293 170 59 39 544 156 56 281 236 240 -.111 .8 0
14 -.23 21210 155 66 57 19 100 55 58 40 551 156 55 96 69 59 -1.258 .33 0
15 -1.039 21105 870 471 57 19 525 303 57 39 593 156 54 504 884 430 -.852 .92 0
16 -.482 21000 138 57 59 19 76 43 57 37 600 156 54 73 45 32 -2.053 .11 0
17 -.347 20895 299 156 60 19 223 132 55 38 576 156 52 214 225 177 -.561 .81 0
18 -1.383 20790 2834 1464 58 18 1578 969 54 39 576 156 51 1517 3321 1273 -.921 .95 0
19 -.1 20685 6580 3934 58 22 10390 6156 54 39 576 156 51 9990 8500 7930 .608 .98 0
20 -.292 20580 589 328 58 22 553 365 56 38 576 156 53 531 568 464 -.152 .92 0

Total number of rows: 22575

Table truncated, full table size 1747 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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