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Sample GSM661696 Query DataSets for GSM661696
Status Public on Aug 15, 2011
Title BALBc_p53null_spontaneous_4702L_MEDINA
Sample type RNA
 
Channel 1
Source name whole mouse reference RNA
Organism Mus musculus
Characteristics reference: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups
Biomaterial provider Cam Patterson - UNC
Extracted molecule total RNA
Extraction protocol Total RNA isolated by Trizol
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
Channel 2
Source name BALBc_p53null_spontaneous_4702L_MEDINA
Organism Mus musculus
Characteristics strain: BALBc
tumor: mammary tumor
pathology: N/A
latency: 56 wk
molecular subtype: Basal 1
Extracted molecule total RNA
Extraction protocol Qiagen Rneasy Mini Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-124
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-524
Scan protocol scanned on Agilent scanner (model G2505B)
Description mammary tumor
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Jan 26, 2011
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 (2)
GSE27101 Comparative oncogenomics identifies breast tumors enriched in functional tumor initiating cells
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
VALUE log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN)
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 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 -.339 190 82 106 50 101 78 58 46 521 156 47 82 67 53 -1.262 .41 0
2 -.479 184 63 108 40 94 62 62 50 576 156 50 76 58 41 -1.548 .14 0
3 -.344 223 86 110 40 129 75 59 48 600 156 47 104 100 78 -.989 .35 0
4 -.357 182 66 111 42 88 58 56 43 600 156 45 71 53 42 -1.45 .12 0
5 -.426 2534 1473 111 41 3162 1978 54 42 576 156 43 2570 3180 2367 .061 .98 0
6 -3.08 533 308 109 37 102 61 53 42 576 156 43 82 419 49 -3.442 .39 0
7 -.29 182 64 111 43 89 55 55 44 576 156 44 72 54 44 -1.344 .19 0
8 -1.918 485 237 113 43 170 96 59 46 576 156 47 138 394 104 -2.029 .7 0
9 -1.429 192 77 114 42 73 43 59 46 600 156 47 59 54 20 -2.699 .08 0
10 -.219 205 87 112 38 115 78 58 48 600 156 47 93 78 67 -1.014 .38 0
11 .126 260 108 112 38 222 148 59 44 576 156 47 180 148 162 -.154 .7 0
12 -.276 212 88 110 39 123 82 60 44 576 156 48 100 88 72 -.971 .4 0
13 -.186 279 112 110 38 209 136 57 45 576 156 46 169 170 150 -.458 .7 0
14 -.035 181 70 111 39 95 58 53 42 576 156 43 77 54 53 -1.041 .25 0
15 -.395 574 299 111 37 551 335 55 41 600 156 44 447 549 417 -.201 .91 0
16 -.34 181 63 112 37 88 53 57 41 600 156 46 71 52 41 -1.466 .19 0
17 -.341 283 120 112 36 191 124 56 42 576 156 45 155 170 135 -.637 .66 0
18 -.642 1924 1067 112 38 1992 1193 56 45 576 156 45 1619 2339 1499 -.203 .97 0
19 -.834 5484 3167 114 40 5490 3286 56 43 576 156 45 4463 7212 4045 -.281 .99 0
20 -.447 490 232 115 41 427 262 57 43 576 156 46 347 434 318 -.317 .86 0

Total number of rows: 22575

Table truncated, full table size 1630 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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