NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM988577 Query DataSets for GSM988577
Status Public on Oct 01, 2015
Title Strain_p53-/- jnk1+/+ jnk2+/+_3929_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_Jnk2wt_3929_tumor
Organism Mus musculus
Characteristics tissue type: mammary tumor
genotype/variation: Trp53ko
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 .659 1 16240 2467 15 9 18180 1693 34 18 10482 72 72 38680 13654 21563 1.251 -1 0
2 1.224 2 21 13 15 9 41 24 34 18 8534 86 72 87 4 11 1.585 -1 0
3 .399 3 25 14 15 9 40 20 34 18 7282 86 72 85 7 9 .7 -1 0
4 -.694 4 28 14 15 9 37 14 34 18 7302 82 72 78 9 5 -.876 .34 0
5 0 5 20 11 15 9 33 17 34 18 7166 84 72 70 0 0 0 -1 0
6 -1.792 6 23 14 15 9 34 15 34 17 7212 80 72 72 4 1 0 -1 0
7 .458 7 21 12 15 10 37 18 33 17 7228 84 70 78 4 6 1 .24 0
8 -2.23 8 26 15 15 9 33 16 33 17 7356 82 70 70 6 1 0 .43 0
9 .554 9 23 11 15 10 39 19 33 18 7284 88 70 82 6 8 1 -1 0
10 -.002 10 29 16 15 10 40 21 33 17 7212 94 70 85 10 10 .322 -1 0
11 -1.673 11 23 12 15 9 33 14 33 17 7296 80 70 70 4 1 0 .13 0
12 .63 12 23 13 15 9 39 20 33 17 7296 86 70 82 5 8 1 -1 0
13 .743 13 25 16 15 9 41 19 33 17 7196 84 70 87 7 12 1.087 -1 0
14 .855 14 21 11 15 9 38 17 33 17 7104 84 70 80 4 7 1.322 -1 0
15 .521 15 22 10 15 9 37 21 33 17 7220 76 70 78 4 6 .678 -1 0
16 -1.503 16 31 18 15 9 35 15 33 17 7174 84 70 74 11 3 -1.806 -1 0
17 .409 17 24 12 15 9 38 17 33 17 7158 86 70 80 6 8 .515 .4 0
18 .802 18 24 11 15 9 41 20 33 17 7094 88 70 87 6 11 1.28 .42 0
19 .949 19 22 13 15 9 39 19 33 17 7182 82 70 82 5 9 1.263 .41 0
20 0 20 22 11 15 10 33 15 34 17 7236 84 72 70 0 0 0 -1 0

Total number of rows: 180880

Table truncated, full table size 12953 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap