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Sample GSM988569 Query DataSets for GSM988569
Status Public on Oct 01, 2015
Title Strain_p53-/- jnk1+/+ jnk2-/-_7970_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_7970_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 -.869 1 14062 1247 17 10 7315 1661 32 17 10308 78 54 12398 13667 7485 -.186 .22 0
2 -.51 2 26 13 17 10 36 21 33 18 8532 90 55 61 7 5 0 .57 0
3 -.155 3 24 13 18 11 36 24 33 18 7190 86 55 61 4 4 .585 -1 0
4 0 4 20 11 18 11 30 17 32 18 7278 84 54 50 0 0 0 .19 0
5 0 5 24 10 18 10 32 14 33 18 7236 82 55 54 0 0 0 .46 0
6 .532 6 22 13 17 10 37 18 32 17 7188 82 54 62 4 6 1.415 .28 0
7 .582 7 31 18 17 10 44 24 32 17 7246 94 54 74 10 16 .737 .07 0
8 -1.937 8 25 13 17 10 33 18 32 17 7126 90 54 55 6 1 -2.322 .19 0
9 -.137 9 25 11 17 10 36 23 32 17 7034 84 54 61 6 6 .223 -1 0
10 1.168 10 18 10 17 10 33 16 32 17 7264 88 54 55 1 2 0 .22 0
11 .51 11 23 11 17 10 37 18 32 17 7222 86 54 62 4 6 1.415 .57 0
12 -1.24 12 26 14 17 10 34 19 32 17 7016 88 54 57 7 2 -1 .34 0
13 .624 13 23 11 17 10 38 19 32 17 7156 88 54 64 5 8 1.322 .38 0
14 1.256 14 20 13 17 10 36 17 32 17 7096 78 54 61 2 5 0 .31 0
15 -3.05 15 26 14 17 10 32 16 32 17 7180 88 54 54 6 0 0 .58 0
16 .577 16 23 11 17 10 37 22 32 17 7206 86 54 62 5 7 1 -1 0
17 1.146 17 21 11 17 10 38 15 32 17 7210 86 54 64 3 7 2.322 -1 0
18 1.518 18 22 13 17 10 42 24 32 17 7094 84 54 71 4 13 2.503 .4 0
19 -.824 19 26 15 17 11 35 12 32 17 7026 78 54 59 7 4 -.264 -1 0
20 1.234 20 24 15 17 11 42 21 32 17 7034 82 54 71 5 13 1.766 -1 0

Total number of rows: 180880

Table truncated, full table size 12886 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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