NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM211526 Query DataSets for GSM211526
Status Public on Jan 18, 2008
Title Brg1+/- murine mammary tumor (MIXED_Brg1het_T55_BULTMAN)
Sample type RNA
 
Channel 1
Source name Mouse Reference
Organism Mus musculus
Characteristics Whole mouse total RNA
Biomaterial provider Cam Patterson-UNC-CH
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 MIXED_Brg1het_T55_BULTMAN
Organism Mus musculus
Characteristics primary mammary tumor
Biomaterial provider Scott Bultman - UNC
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 MIXED_Brg1het_T55_BULTMAN
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Jul 18, 2007
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 GPL2881
Series (2)
GSE8516 Characterization of mammary tumors from Brg1 heterozygous mice
GSE65677 The Six1 oncoprotein represses translation of p53 via concomitant regulation of RPL26 and microRNA-27a

Data table header descriptions
ID_REF Spot Reference ID
LOG_RAT2N_MEAN log2_ratio of channel 2 normalized over channel 1
SPOT spot number on array
CH1_MEAN channel 1 mean intensity
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
VALUE same as UNF_VALUE but with flagged values removed
CORR correlation coefficient among pixels
FLAG Spot flag. 0:not flagged; negative:Flagged as bad spots; positive:flagged as good spots
CONTROL Y: control gene; N: not control
UNF_VALUE LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN

Data table
ID_REF LOG_RAT2N_MEAN 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 VALUE CORR FLAG CONTROL UNF_VALUE
1 -1.218 22575 156 61 77 370 94 53 60 39 550 156 60 94 51 51 -.005 -1 0 Y -.005
2 -1.404 22470 161 67 79 33 90 52 59 41 576 156 59 90 53 47 -.166 .15 0 Y -.166
3 -.608 22365 202 85 77 30 139 85 58 39 600 156 58 140 99 101 .022 .46 0 N .022
4 -1.355 22260 165 67 78 29 93 52 59 40 600 156 59 93 58 50 -.19 .24 0 N -.19
5 -.589 22155 3007 1716 78 29 1989 1125 61 45 576 156 61 2009 3534 1597 -1.145 .97 0 N -1.145
6 -2.556 22050 488 291 76 28 130 74 61 43 576 156 61 131 365 77 -2.229 .5 0 N -2.229
7 1.322 21945 83 36 77 52 74 39 59 41 576 156 59 74 6 13 .928 .08 0 Y .928
8 -2.506 21840 459 230 78 48 125 68 59 45 576 156 59 126 333 75 -2.145 .48 0 N -2.145
9 -.969 21735 166 70 78 30 103 59 59 41 600 156 59 104 61 63 .039 .23 0 N .039
10 -.165 21630 180 79 78 29 150 88 60 39 600 156 60 151 80 113 .498 .51 0 N .498
11 -.826 21525 259 121 78 32 163 83 62 41 576 156 62 164 153 119 -.367 .56 0 N -.367
12 -1.083 21420 207 85 80 33 120 68 61 40 576 156 61 121 97 76 -.357 .41 0 N -.357
13 -.454 21315 268 121 79 30 197 112 60 38 576 156 60 198 165 156 -.089 .6 0 N -.089
14 -.876 21210 189 75 77 29 121 76 61 40 576 156 61 122 85 78 -.109 .41 0 Y -.109
15 .149 21105 363 194 78 29 375 227 62 42 600 156 62 378 279 319 .191 .85 0 N .191
16 -1.165 21000 160 66 77 29 99 57 63 41 600 156 63 100 55 53 -.044 .26 0 N -.044
17 .952 20895 277 133 76 28 448 260 63 40 576 156 63 452 194 396 1.025 .84 0 N 1.025
18 -.565 20790 1531 767 77 28 1032 584 59 40 576 156 59 1042 1652 856 -.949 .95 0 N -.949
19 .134 20685 5608 3431 78 28 6061 3648 58 39 576 156 58 6122 7087 4683 -.598 .98 0 N -.598
20 -.411 20580 554 295 78 30 412 228 58 38 576 156 58 416 487 345 -.498 .89 0 N -.498

Total number of rows: 22575

Table truncated, full table size 1915 Kbytes.




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