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Sample GSM988574 Query DataSets for GSM988574
Status Public on Oct 01, 2015
Title Strain_p53-/- jnk1+/+ jnk2-/-_9003_Van_Den_Berg
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_9003_tumor
Organism Mus musculus
Characteristics tissue type: mammary tumor
genotype/variation: Trp53ko, Jnk2ko
strain: 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 .259 1 9950 1722 19 11 13964 2020 34 18 10448 88 35 14545 10751 12868 .547 .49 0
2 -.661 2 30 16 19 12 40 18 34 18 8570 80 35 41 10 6 -.415 -1 0
3 .179 3 23 12 20 12 38 23 35 18 7194 84 36 39 3 3 1.585 -1 0
4 .5 4 25 12 19 12 44 19 35 18 7158 84 36 45 6 9 1.17 .22 0
5 -1.161 5 26 12 20 12 37 19 35 18 7296 86 36 38 6 2 -1 -1 0
6 0 6 22 12 20 12 33 17 35 18 7310 86 36 34 0 0 0 .32 0
7 .891 7 25 13 20 12 44 24 35 18 7130 88 36 45 5 9 1.585 -1 0
8 .833 8 21 10 19 12 38 17 34 17 7128 86 35 39 2 4 0 -1 0
9 .587 9 23 13 19 12 40 20 34 17 7116 88 35 41 4 6 2.585 .13 0
10 -1.238 10 23 12 19 12 36 17 34 17 7152 92 35 37 5 2 0 -1 0
11 0 11 24 13 20 12 34 16 34 17 7130 86 35 35 0 0 0 .25 0
12 0 12 21 12 19 12 33 16 34 17 7176 88 35 34 0 0 0 -1 0
13 .064 13 25 12 20 11 39 19 34 18 7264 90 35 40 5 5 .322 .42 0
14 -.275 14 24 11 20 11 37 18 34 18 7178 80 35 38 4 3 .585 -1 0
15 -.49 15 23 15 20 12 36 20 34 18 7384 86 35 37 3 2 1 -1 0
16 1.523 16 23 11 20 12 45 20 35 18 7334 86 36 46 3 10 3.322 .2 0
17 -.965 17 30 18 20 12 40 24 35 18 7238 82 36 41 10 5 -.678 .14 0
18 .559 18 24 13 20 12 41 21 35 18 7258 80 36 42 4 6 1.585 -1 0
19 .991 19 25 15 20 12 45 25 35 18 7204 90 36 46 5 10 1.737 .17 0
20 0 20 25 12 19 11 30 16 35 18 7154 80 36 31 0 0 0 .17 0

Total number of rows: 180880

Table truncated, full table size 12819 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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