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Sample GSM855893 Query DataSets for GSM855893
Status Public on Jun 25, 2012
Title T9_Kp16null_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 T9_Kp16null_rep
Organism Mus musculus
Characteristics tumor: KRAS; p16 null (TKp16L/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 -.255 1 38894 2731 27 14 24789 1861 38 19 10554 74 52 34429 33882 28392 -.176 .55 0
2 -1.39 2 43 14 28 14 42 24 38 19 8652 76 52 58 12 4 -1.114 -1 0
3 -.095 3 36 18 29 15 43 14 38 20 7302 86 52 59 6 6 .223 .43 0
4 -6.668 4 40 22 29 14 38 23 38 20 7396 90 52 52 9 0 0 .15 0
5 1.143 5 34 14 29 15 47 23 38 20 7246 80 52 65 5 11 2.115 .53 0
6 .864 6 35 16 29 15 47 22 38 19 7194 84 52 65 5 10 1.7 .39 0
7 .95 7 35 12 29 15 46 23 38 19 7244 78 52 63 5 10 1.459 .35 0
8 .471 8 39 18 29 15 48 20 38 19 7334 84 52 66 8 11 .807 .22 0
9 -.983 9 33 16 29 14 39 19 38 19 7094 84 52 54 3 1 -.584 .46 0
10 1.549 10 34 12 29 15 49 21 38 19 7176 92 52 68 4 12 2.415 -1 0
11 1.127 11 34 15 29 15 46 22 38 19 7276 82 52 63 4 10 1.875 -1 0
12 .579 12 38 20 29 15 48 21 38 20 7284 88 52 66 7 11 1.222 .56 0
13 -.376 13 37 17 29 15 43 26 38 19 7108 84 52 59 7 5 .223 -1 0
14 .495 14 38 18 29 15 47 24 38 19 7354 84 52 65 8 11 .893 .34 0
15 1.638 15 32 15 29 15 46 17 38 19 7250 90 52 63 2 9 3.459 -1 0
16 .219 16 37 17 28 15 46 22 38 19 7234 84 52 63 8 9 .874 -1 0
17 -.542 17 36 19 28 15 42 19 38 19 7262 82 52 58 7 5 .263 .32 0
18 -1.558 18 41 12 28 15 41 15 38 19 7236 80 52 56 11 3 -1.322 .37 0
19 -1.062 19 38 19 28 15 41 20 38 19 7272 86 52 56 9 4 -.808 -1 0
20 1.805 20 32 17 28 15 50 20 38 19 7332 88 52 69 4 14 4.087 -1 0

Total number of rows: 180880

Table truncated, full table size 13302 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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