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Sample GSM571051 Query DataSets for GSM571051
Status Public on Jan 22, 2011
Title BALB_C4-HD_3_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, 38:121-147
 
Channel 2
Source name BALB_C4-HD_3_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, 38:121-147
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_3_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 -6.822 22575 4016 2394 46 14 88 54 56 41 521 156 57 89 3790 33 -6.966 .24 0 -6.822
2 .196 22470 91 33 48 14 80 45 58 41 544 156 59 81 28 32 -.966 .05 0 .196
3 .568 22365 106 43 47 14 109 64 57 41 568 156 58 111 45 67 -.155 .33 0 .568
4 .051 22260 100 35 46 17 85 49 56 40 568 156 57 86 38 40 -.897 .13 0 .051
5 .831 22155 1447 760 46 16 3199 1838 57 39 544 156 58 3264 1572 2798 1.194 .97 0 .831
6 -2.305 22050 351 172 46 13 102 64 57 40 544 156 58 104 260 52 -2.727 .36 0 -2.305
7 -.055 21945 47 12 45 14 66 43 57 42 544 156 58 67 4 4 2.17 .04 0 -.055
8 .101 21840 296 147 46 14 285 172 56 42 544 156 57 290 231 247 -.102 .82 0 .101
9 .4 21735 89 34 46 14 82 46 55 41 568 156 56 83 29 39 -.671 .15 0 .4
10 .136 21630 116 47 45 13 104 66 57 42 568 156 58 106 55 60 -.565 .29 0 .136
11 -1.059 21525 185 92 45 14 105 65 61 46 544 156 62 107 113 54 -1.639 .34 0 -1.059
12 .2 21420 125 47 46 13 116 71 59 41 544 156 60 118 62 71 -.446 .46 0 .2
13 -.187 21315 189 77 46 14 150 93 59 41 544 156 60 153 121 106 -.621 .57 0 -.187
14 .515 21210 101 39 46 14 100 58 55 42 544 156 56 102 41 59 -.258 .24 0 .515
15 .132 21105 269 135 46 14 262 164 58 42 570 156 59 267 203 223 -.1 .78 0 .132
16 .063 21000 92 33 47 14 76 50 55 41 570 156 56 77 30 31 -1.099 .13 0 .063
17 .167 20895 182 88 46 14 164 111 51 38 544 156 52 167 116 131 -.241 .66 0 .167
18 -.097 20790 1316 1668 47 13 1424 2946 55 37 551 156 56 1453 1363 1274 .139 .74 0 -.097
19 -1.377 20685 4537 2554 47 13 2408 1537 57 41 569 156 58 2457 5235 2016 -.905 .95 0 -1.377
20 .342 20580 482 251 46 13 586 359 57 41 576 156 58 597 426 540 .306 .92 0 .342

Total number of rows: 22575

Table truncated, full table size 1850 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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