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Sample GSM571052 Query DataSets for GSM571052
Status Public on Jan 22, 2011
Title BALB_C4-HD_4_FIB_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, 38:121-148
 
Channel 2
Source name BALB_C4-HD_4_FIB_LCM
Organism Mus musculus
Characteristics strain: BALB/c
tissue: laser captured tumor stroma
Biomaterial provider Claudia Lanari - Instituto de Biología y Medicina Experimental , Argentina
Treatment protocol MPA treatment
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, 38:121-148
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-HD_4_FIB_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 -7.453 22575 6187 3873 53 18 82 45 52 39 521 156 57 91 5677 32 -7.381 .16 0 -7.453
2 .902 22470 103 40 55 19 78 49 52 36 544 156 57 86 25 48 -.727 .05 0 .902
3 .674 22365 152 67 55 19 137 86 56 38 568 156 62 152 70 111 -.108 .53 0 .674
4 .394 22260 131 51 55 20 97 52 57 36 568 156 63 107 48 63 -.788 .28 0 .394
5 1.403 22155 1988 1075 55 20 7169 4157 55 35 544 156 61 7965 2280 6029 2.032 .97 0 1.403
6 -2.521 22050 456 241 54 19 99 62 56 37 544 156 62 110 314 54 -3.071 .38 0 -2.521
7 -.805 21945 61 22 55 30 63 35 56 40 544 156 62 70 8 4 .415 -1 0 -.805
8 .833 21840 298 159 55 31 391 250 57 41 544 156 63 434 213 380 .611 .88 0 .833
9 21735 316 1765 55 20 84 65 59 38 568 156 65 93 184 35 -3.224 .14 -100 -2.386
10 .206 21630 142 61 55 20 102 62 59 39 570 156 65 113 56 65 -.857 .27 0 .206
11 -.848 21525 241 112 55 20 114 66 56 39 544 156 62 126 139 77 -1.54 .48 0 -.848
12 -.058 21420 150 57 55 18 96 54 57 36 544 156 63 106 62 59 -1.142 .3 0 -.058
13 .055 21315 234 113 56 71 175 101 58 41 544 156 64 194 141 147 -.454 .62 0 .055
14 .384 21210 553 3288 57 71 640 4802 56 42 551 156 62 711 471 614 .387 .58 0 .384
15 .959 21105 389 192 56 20 610 361 55 40 593 156 61 677 308 599 .888 .9 0 .959
16 .095 21000 119 47 55 19 77 50 57 41 600 156 63 85 34 36 -1.54 .13 0 .095
17 1.274 20895 295 151 55 19 524 337 56 41 576 156 62 582 215 521 1.116 .88 0 1.274
18 .139 20790 1708 1016 56 743 2221 1390 51 42 576 156 56 2467 1804 1986 .545 .97 0 .139
19 -.459 20685 5644 3599 56 25 6338 4321 51 40 576 156 56 7042 6949 5055 .322 .98 0 -.459
20 .082 20580 570 304 58 19 534 328 54 36 576 156 60 593 481 510 .058 .92 0 .082

Total number of rows: 22575

Table truncated, full table size 1875 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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