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Sample GSM855024 Query DataSets for GSM855024
Status Public on Jun 25, 2012
Title C10_Kp53null
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 Charles Perou - UNC
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen RNeasy Kit
Label Cy3
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
Channel 2
Source name C10_Kp53null
Organism Mus musculus
Characteristics tumor: KRAS; p53 null; Lkb1 null with Lkb1 add back (TKp53L/LLkb1L/L + pBabe_Lkb1)
Extracted molecule total RNA
Extraction protocol Total RNA isolated using Qiagen Rneasy Kit
Label Cy5
Label protocol described in Hu et al., 2005, BioTechniques, 38:121-125
 
 
Hybridization protocol described in Hu et al., 2005, BioTechniques, 38:121-125
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software v10.7.3.1
Description Cell Line
Data processing Data for both channels were Lowess-normalized and then the log(2) ratio was taken
 
Submission date Dec 29, 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 GPL11383
Series (1)
GSE34866 LKB1/STK11 Inactivation Leads to Expansion of Pro-Metastatic Tumor Sub-Population in Melanoma

Data table header descriptions
ID_REF Spot Reference ID
VALUE log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN)
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

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
1 -1.627 1 33332 2698 21 12 27640 1639 37 21 10536 76 57 43187 53287 17255 .373 .37 0
2 -.371 2 57 26 22 12 56 32 37 21 8548 90 57 87 29 23 -.138 -1 0
3 -.144 3 44 21 22 12 51 22 37 21 7122 80 57 79 18 17 .068 -1 0
4 -.073 4 48 19 22 13 54 21 37 21 7078 78 57 84 22 21 .17 .24 0
5 .37 5 43 18 22 12 56 27 37 20 7186 84 57 87 17 23 .659 .42 0
6 -2.473 6 42 20 22 12 38 23 38 20 7164 82 59 59 9 1 0 -1 0
7 0 7 37 19 21 12 47 26 38 20 7122 86 59 73 12 12 0 -1 0
8 .071 8 45 21 21 12 55 24 38 20 7226 80 59 85 20 21 .308 .32 0
9 -.491 9 44 23 21 12 48 23 38 20 7134 86 59 75 18 13 -.322 .4 0
10 -.638 10 47 22 21 12 48 22 37 20 7040 90 57 75 21 14 -.415 .43 0
11 -1.041 11 43 16 22 13 43 26 38 21 7158 88 59 67 15 7 -1.248 .66 0
12 -.845 12 44 20 22 12 45 25 38 21 7172 94 59 70 17 9 -.932 .35 0
13 -.365 13 42 13 22 12 48 23 38 21 7242 80 59 75 16 12 -.248 -1 0
14 -.617 14 47 21 21 13 49 20 38 21 7226 80 59 76 21 14 -.436 -1 0
15 -.557 15 42 20 21 13 46 25 38 21 7196 88 59 71 16 11 -.584 -1 0
16 -2.457 16 51 21 21 13 39 13 37 21 7182 90 57 60 20 3 -3.224 .21 0
17 -.231 17 43 16 21 12 49 25 37 21 7230 84 57 76 17 15 0 .21 0
18 .066 18 42 19 21 12 53 24 38 21 7296 88 59 82 17 18 .276 -1 0
19 -.754 19 47 22 21 12 47 19 37 21 7200 78 57 73 21 12 -.584 -1 0
20 -.973 20 53 25 21 12 48 29 37 21 7126 92 57 75 26 13 -.737 -1 0

Total number of rows: 180880

Table truncated, full table size 13400 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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