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Sample GSM571048 Query DataSets for GSM571048
Status Public on Jan 22, 2011
Title BALB_C4-HI_3_EPI_LCM
Sample type RNA
 
Channel 1
Source name Mouse Reference
Organism Mus musculus
Characteristics strain: BALB/c
tissue: whole mouse total RNA
Biomaterial provider Cam Patterson-UNC-CH
Extracted molecule total RNA
Extraction protocol Total RNA isolated by TRIZOL reagent
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-144
 
Channel 2
Source name BALB_C4-HI_3_EPI_LCM
Organism Mus musculus
Characteristics strain: BALB/c
tissue: laser captured epithelial tumor cells
Biomaterial provider Claudia Lanari - Instituto de Biología y Medicina Experimental , Argentina
Extracted molecule total RNA
Extraction protocol Stratagene RNA microisolation kit (Stratagene, La Jolla, CA)
Label Cy5
Label protocol see methods
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-144
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 BALB_C4-HI_3_EPI_LCM
Data processing Data for both channels were Lowess-normalized and then log(2) ratio was taken
 
Submission date Jul 27, 2010
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 (1)
GSE23214 MPA-induced gene expression and stromal and parenchymal gene expression profiles in luminal murine mammary tumors with different hormonal requirements

Data table header descriptions
ID_REF Spot Reference ID
VALUE same as UNF_VALUE but with flagged values removed
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
UNF_VALUE log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN)

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 UNF_VALUE
1 -7.981 22575 4193 2544 65 23 80 57 62 47 521 156 45 58 4333 17 -8.381 .08 0 -7.981
2 .205 22470 122 47 65 24 81 52 60 44 544 156 43 59 32 37 -1.831 .14 0 .205
3 .8 22365 135 55 65 22 123 80 59 41 568 156 43 89 50 88 -.606 .38 0 .8
4 .243 22260 122 42 64 21 85 51 62 42 568 156 45 62 33 39 -1.771 .17 0 .243
5 1.256 22155 1327 738 65 21 6927 4207 59 41 544 156 43 5056 1905 4549 1.99 .96 0 1.256
6 -2.218 22050 350 190 66 23 100 62 57 42 544 156 41 72 238 51 -3.198 .3 0 -2.218
7 1.612 21945 105 431 66 23 103 446 58 43 544 156 42 75 23 73 -.241 .05 0 1.612
8 -.199 21840 278 143 65 23 233 147 58 43 544 156 42 170 206 180 -.735 .77 0 -.199
9 .42 21735 123 50 68 24 86 54 61 43 568 156 44 62 32 42 -1.613 .11 0 .42
10 .216 21630 148 61 69 24 104 62 59 42 568 156 43 75 55 64 -1.304 .25 0 .216
11 -.804 21525 234 107 66 33 127 78 61 43 544 156 44 92 139 79 -1.806 .48 0 -.804
12 -.219 21420 157 61 66 33 101 58 63 44 544 156 45 73 63 54 -1.699 .3 0 -.219
13 -.225 21315 245 105 65 24 195 128 66 43 544 156 48 142 164 140 -.938 .65 0 -.225
14 -.302 21210 147 57 65 25 88 58 60 44 568 156 43 64 53 43 -1.966 .18 0 -.302
15 .772 21105 347 178 67 23 674 449 57 43 568 156 41 491 318 543 .684 .88 0 .772
16 -.376 21000 138 55 67 22 77 48 59 40 544 156 43 56 40 31 -2.45 .09 0 -.376
17 .212 20895 230 110 67 23 225 137 61 43 544 156 44 164 151 175 -.442 .76 0 .212
18 -.923 20790 1052 652 67 22 912 605 63 44 544 156 45 665 1259 664 -.669 .94 0 -.923
19 -.515 20685 4477 2679 66 22 8652 5774 61 41 544 156 44 6315 7358 5149 .508 .95 0 -.515
20 -.346 20580 413 204 67 25 384 256 58 44 568 156 42 280 378 297 -.54 .83 0 -.346

Total number of rows: 22575

Table truncated, full table size 1864 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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