NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM804363 Query DataSets for GSM804363
Status Public on Jan 31, 2021
Title STRAIN_MMTV_Neu_2T3_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 -7.868 22575 5440 2867 163 40 78 55 48 33 521 156 40 65 6082 26 -7.644 .24 0
2 -.276 22470 212 57 166 79 69 49 47 34 544 156 39 57 35 28 -1.355 .14 0
3 1.07 22365 233 56 169 77 162 94 51 36 568 156 42 136 58 122 .555 .29 0
4 -.545 22260 221 61 167 40 75 42 53 36 568 156 44 63 41 28 -1.506 .11 0
5 -1.655 22155 1741 859 163 41 796 456 54 33 544 156 45 668 1920 609 -1.34 .96 0
6 -2.946 22050 466 190 166 48 89 56 54 33 544 156 45 74 284 36 -3.366 .29 0
7 .207 21945 168 38 166 49 61 32 55 35 544 156 46 51 3 3 1.322 .06 0
8 -2.558 21840 377 123 164 46 81 50 52 36 544 156 43 68 190 32 -3.095 .18 0
9 -.074 21735 214 58 168 46 78 43 52 35 568 156 43 65 35 33 -1.065 .14 0
10 .092 21630 239 68 170 40 105 56 52 33 568 156 43 88 58 62 -.617 .29 0
11 .122 21525 308 90 168 45 212 113 52 36 544 156 43 178 143 156 -.053 .73 0
12 -.759 21420 256 65 169 82 87 53 51 37 544 156 42 73 72 43 -1.49 .27 0
13 .559 21315 306 87 169 77 275 165 51 32 544 156 42 231 144 212 .465 .55 0
14 -.049 21210 234 60 166 39 98 54 52 30 544 156 43 82 56 54 -.801 .26 0
15 -.07 21105 407 134 163 38 339 191 52 33 568 156 43 284 271 258 -.017 .83 0
16 -.56 21000 220 57 162 40 75 40 51 34 568 156 42 63 45 30 -1.466 .12 0
17 .207 20895 276 79 163 41 176 112 51 34 544 156 42 147 110 127 -.106 .58 0
18 -1.656 20790 1282 611 161 41 559 319 51 34 544 156 42 469 1339 425 -1.392 .94 0
19 -.872 20685 5244 2659 165 46 4819 2485 50 32 544 156 42 4049 6659 3637 -.342 .99 0
20 -.116 20580 458 165 165 45 398 221 52 33 544 156 43 334 331 305 -.01 .86 0

Total number of rows: 22575

Table truncated, full table size 1762 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap