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Sample GSM855884 Query DataSets for GSM855884
Status Public on Jun 25, 2012
Title T3_Kp53Lkb1null_rep
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 T3_Kp53Lkb1null_rep
Organism Mus musculus
Characteristics tumor: KRAS; p53 null, Lkb1 null (TKp53L/LLkb1L/L)
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 Tumor
Data processing Data for both channels were Lowess-normalized and then the log(2) ratio was taken
 
Submission date Jan 03, 2012
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 -.722 1 37781 3174 23 13 40525 4169 37 22 10464 80 37 40934 50210 30447 .115 .33 0
2 .132 2 48 21 24 13 62 30 37 21 8644 92 37 62 23 26 .184 .27 0
3 .258 3 35 18 25 13 49 24 37 21 7240 84 37 49 10 12 .585 -1 0
4 -.231 4 46 19 25 13 54 25 37 21 7408 88 37 54 20 17 -.16 -1 0
5 -.919 5 38 19 25 14 44 18 37 21 7422 78 37 44 13 7 -.653 .28 0
6 -1.555 6 39 18 25 14 41 22 37 21 7362 90 37 41 14 4 -1.458 -1 0
7 .371 7 34 16 25 13 48 27 37 21 7392 84 37 48 9 11 .652 .37 0
8 .281 8 35 13 25 13 49 26 37 21 7432 78 37 49 10 12 .585 -1 0
9 -.421 9 40 20 25 13 47 25 36 21 7264 78 36 47 15 11 -.241 .34 0
10 -.55 10 40 17 25 13 47 22 37 21 7232 84 37 47 14 10 -.379 -1 0
11 -.452 11 37 19 24 13 46 23 37 21 7566 84 37 46 13 9 -.29 -1 0
12 -.738 12 34 14 24 13 43 26 37 21 7372 82 37 43 10 6 -.415 -1 0
13 -1.416 13 38 16 24 13 42 21 37 21 7278 86 37 42 14 5 -1.262 -1 0
14 -1.396 14 39 17 25 13 42 26 37 21 7346 84 37 42 14 5 -1.377 -1 0
15 .63 15 35 14 25 13 53 24 37 21 7372 82 37 53 10 16 .83 .29 0
16 -.334 16 37 16 24 13 47 22 37 21 7416 88 37 47 13 10 -.138 -1 0
17 -.324 17 40 20 25 13 50 26 38 22 7402 84 38 50 15 12 -.223 .17 0
18 -.458 18 40 23 24 13 49 22 38 21 7496 88 38 49 16 11 -.241 .44 0
19 -.272 19 36 14 24 13 48 20 38 21 7348 86 38 48 12 10 0 .15 0
20 .122 20 40 23 24 13 55 26 38 21 7334 84 38 55 16 17 .28 -1 0

Total number of rows: 180880

Table truncated, full table size 13274 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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