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Sample GSM988582 Query DataSets for GSM988582
Status Public on Oct 01, 2015
Title C1_p53null_jnk2null
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 BALB/c_Trp53ko_Jnk2ko_cell_line
Organism Mus musculus
Characteristics tissue type: cell line
genotype/variation: Trp53ko, Jnk2ko
cell line origin: BALB/c
Biomaterial provider Carla Van Den Berg - Univ. of Texas at Austin
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
Data processing Data for both channels were Lowess-normalized and then the log(2) ratio was taken
 
Submission date Aug 20, 2012
Last update date Oct 01, 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)
GSE40226 JNK2 inhibits mammary luminal cell commitment

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 -1.565 1 40352 3490 21 12 23965 2008 39 20 10520 76 15 9586 53428 18061 -2.077 .73 0
2 -.358 2 59 24 22 12 96 28 38 20 8518 86 15 38 52 41 -.606 .44 0
3 -.055 3 50 23 23 12 98 30 38 20 7160 88 15 39 41 40 -.059 .27 0
4 -.008 4 44 19 22 12 94 34 38 19 7168 88 15 37 35 35 .212 -1 0
5 .013 5 53 19 23 12 101 30 37 19 7046 84 14 40 44 44 -.106 .49 0
6 .179 6 51 22 23 12 105 38 37 19 7066 74 14 42 41 47 .107 .3 0
7 .136 7 49 25 23 12 102 35 38 19 7056 86 15 40 39 42 .059 -1 0
8 .047 8 47 23 23 12 98 40 38 19 7174 74 15 39 37 39 .126 .14 0
9 -.104 9 61 22 23 13 104 33 37 19 7158 84 14 41 52 49 -.415 .13 0
10 -.13 10 46 22 23 13 92 30 37 19 7110 80 14 36 38 34 .068 .44 0
11 .075 11 38 20 23 13 88 26 37 19 7092 78 14 35 27 28 .807 .23 0
12 -.162 12 63 25 23 12 103 28 37 19 7108 84 14 41 55 49 -.492 .15 0
13 .232 13 51 20 23 12 107 40 38 20 7076 90 15 42 40 47 .054 .38 0
14 -.195 14 58 20 23 12 99 31 38 20 7182 88 15 39 49 43 -.46 .03 0
15 .254 15 48 16 23 12 106 27 39 20 7206 80 15 42 37 45 .231 -1 0
16 .01 16 44 20 23 12 94 27 38 19 7140 80 15 37 34 34 .212 .43 0
17 .017 17 59 17 23 12 107 33 38 20 7122 76 15 42 49 50 -.333 -1 0
18 .299 18 47 24 23 12 106 28 38 20 7202 78 15 42 36 45 .295 -1 0
19 .23 19 52 23 23 12 108 36 38 20 7196 84 15 43 41 48 .052 -1 0
20 .127 20 53 22 22 12 107 30 38 20 7198 74 15 42 44 48 -.053 .4 0

Total number of rows: 180880

Table truncated, full table size 13471 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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