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Sample GSM988570 Query DataSets for GSM988570
Status Public on Oct 01, 2015
Title Strain_p53-/- jnk1+/+ jnk2-/-_8967_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_8967_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 -.818 1 11060 654 16 9 4844 878 33 17 10474 62 64 9498 9679 5490 -.228 -1 0
2 -1.126 2 23 13 16 10 34 16 33 17 8710 94 64 66 5 2 -1 .27 0
3 -.677 3 25 12 16 10 36 17 33 17 7312 88 64 70 7 4 -.223 .44 0
4 1.127 4 24 13 17 10 40 20 32 17 7276 84 62 78 5 11 1.678 -1 0
5 1.216 5 26 12 17 10 42 22 32 18 7320 86 62 82 6 15 1.515 .31 0
6 0 6 21 11 16 9 28 14 32 17 7138 80 62 54 0 0 0 .27 0
7 1.481 7 22 11 17 10 39 20 32 17 7160 90 62 76 3 10 2.222 .21 0
8 0 8 23 13 17 10 30 15 32 17 7132 92 62 58 0 0 0 .39 0
9 1.401 9 22 13 17 10 40 21 32 17 7218 86 62 78 4 11 2.415 -1 0
10 -.718 10 28 15 17 10 35 17 32 17 7238 90 62 68 8 5 -.584 -1 0
11 -1.41 11 24 12 17 10 33 18 32 17 7074 88 62 64 5 1 -1.322 -1 0
12 -.336 12 27 15 17 10 36 20 32 17 7210 82 62 70 7 5 0 .1 0
13 .646 13 25 12 16 10 40 18 33 17 7262 84 64 78 6 10 1.222 -1 0
14 0 14 23 12 17 10 29 14 33 18 7186 92 64 56 0 0 0 -1 0
15 -2.398 15 22 11 16 10 32 16 32 18 7360 76 62 62 3 0 0 .58 0
16 1.691 16 20 11 16 10 40 14 32 18 7272 78 62 78 3 11 3 -1 0
17 1.284 17 21 13 16 10 39 21 32 18 7264 82 62 76 4 9 2.222 .49 0
18 .668 18 24 13 16 9 39 18 32 17 7114 84 62 76 6 9 1.222 -1 0
19 .722 19 25 13 17 10 39 13 32 17 7104 88 62 76 6 10 1 .45 0
20 -.146 20 22 11 16 10 35 18 32 17 7106 84 62 68 4 4 .585 .32 0

Total number of rows: 180880

Table truncated, full table size 12882 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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