NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM988576 Query DataSets for GSM988576
Status Public on Oct 01, 2015
Title Strain_p53-/- jnk1+/+ jnk2+/+_173_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_173_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 -.387 1 7947 658 14 9 4202 355 32 17 10358 80 72 9550 6579 5029 .257 -1 0
2 -1.014 2 27 17 14 10 34 13 32 17 8618 86 72 77 8 4 -1 .25 0
3 0 3 24 11 14 10 30 15 32 17 7238 88 72 68 0 0 0 .4 0
4 -1.119 4 25 14 15 10 33 14 32 17 7050 84 72 75 6 2 -1.415 .32 0
5 .503 5 24 13 15 10 38 20 32 16 7220 88 72 86 6 9 1 -1 0
6 .619 6 23 13 15 9 38 15 32 17 7126 88 72 86 5 9 1.222 -1 0
7 -1.97 7 26 14 15 9 32 18 32 17 7098 86 72 72 5 1 0 -1 0
8 .671 8 22 13 15 9 36 18 32 18 6996 84 72 81 4 7 .848 -1 0
9 .04 9 23 14 14 9 35 16 32 17 7012 82 72 79 5 6 .223 -1 0
10 .699 10 23 13 14 9 38 17 31 17 7180 80 70 86 6 10 1.193 .57 0
11 1.5 11 21 11 14 9 41 18 32 17 7204 76 71 93 4 13 2.459 .25 0
12 -1.693 12 28 17 14 9 33 18 32 17 7116 80 72 75 8 2 -1.873 -1 0
13 -.375 13 28 19 14 9 37 16 32 17 7008 86 72 84 9 7 .126 .27 0
14 0 14 25 15 15 10 31 15 33 17 7180 82 75 70 0 0 0 .62 0
15 .191 15 25 14 14 9 39 17 33 17 7186 84 75 88 7 8 .53 -1 0
16 0 16 29 18 14 10 32 16 33 17 7112 88 75 72 0 0 0 .16 0
17 1.225 17 22 11 15 9 41 19 33 18 7142 82 75 93 5 12 1.585 .24 0
18 1.301 18 22 13 15 10 40 22 32 18 7248 86 72 90 4 11 1.848 -1 0
19 -.212 19 27 16 15 10 37 18 33 18 7108 86 75 84 8 7 -.152 .51 0
20 .525 20 23 10 15 10 38 13 33 18 7188 88 75 86 5 7 .874 .29 0

Total number of rows: 180880

Table truncated, full table size 12998 Kbytes.




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