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Sample GSM433650 Query DataSets for GSM433650
Status Public on Jul 29, 2009
Title Dermal mRNA expression differences between Casp-8F/–K5-Cre and Casp-8F/+K5-Cre mice.
Sample type RNA
 
Channel 1
Source name Dermis isolated from the skin of Casp-8F/+K5-Cre mouse (P3).
Organism Mus musculus
Characteristics age: P3
tissue: dermis
genotype: Casp-8F/+K5-Cre
pool: total RNA samples from 3 mice were pooled for microarray analysis.
Treatment protocol Skin was removed from the mice and incubated overnight at 4 °C in 2.4 U/ml Dispase (Roche) to separate the epidermis from the dermis.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the RNeasy mini kit from QIAGEN as directed by the manufacturer.
Label Cy3
Label protocol Total RNA was used to prepare Cy3- or Cy5-labeled cRNA by oligo-(dT)-T7-primed double-stranded cDNA synthesis (cDNA Synthesis System, Roche) followed by in-vitro transcription and labeling (Amino Allyl MessageAmp™ II Kit; Ambion) as directed by the manufacturers.
 
Channel 2
Source name Dermis isolated from the skin of Casp-8F/-K5-Cre mouse (P3).
Organism Mus musculus
Characteristics age: P3
tissue: dermis
genotype: Casp-8F/-K5-Cre
pool: total RNA samples from 2 mice were pooled for microarray analysis.
Treatment protocol Skin was removed from the mice and incubated overnight at 4 °C in 2.4 U/ml Dispase (Roche) to separate the epidermis from the dermis.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the RNeasy mini kit from QIAGEN as directed by the manufacturer.
Label Cy5
Label protocol Total RNA was used to prepare Cy3- or Cy5-labeled cRNA by oligo-(dT)-T7-primed double-stranded cDNA synthesis (cDNA Synthesis System, Roche) followed by in-vitro transcription and labeling (Amino Allyl MessageAmp™ II Kit; Ambion) as directed by the manufacturers.
 
 
Hybridization protocol cRNA fragmentation, hybridization and washing steps were performed exactly as recommended by the microarray manufacturer “Two-Color Microarray-Based Gene Expression Analysis Protocol V5.0.1” (see http://www.agilent.com for details).
Scan protocol Slides were scanned on an Affymetrix 428 Array Scanner. The PMT settings were 25 and 35 for the red and the green channel, respectively.
Description M1330-Dermis
Data processing Data were extracted by the use of Imagene V5.0 software (Biodiscovery). Signal median values were corrected by the subtraction of local Background median values. The resulting background-corrected values were left unaltered (red channel values) or, were further processed according to LOWESS-like algorithms (green channel values) to match red channel values throughout the whole intensity range. Only non-control features were considered as input for normalization algorithms applied. Ratio values were calculated by dividing red channel values by green channel values and were log-transformed (base10) thereafter. Data from qualitatively suboptimal spots were flagged and excluded from further analysis if (i) CVsignal mean > 0.20, or (ii) SMglobal background corrected / SMlocal background corrected > 1.3, where 'CVsignal mean' is the coefficient of variance deduced from signal values for all pixels of a spot, and 'SMglobal background corrected / SMlocal background corrected' is the ratio of a global background-corrected signal mean value of a spot divided by its local background-corrected signal mean value.
 
Submission date Jul 27, 2009
Last update date Jul 28, 2009
Contact name Oliver Dittrich-Breiholz
E-mail(s) dittrich.oliver@mh-hannover.de
Organization name Medical School Hannover
Department Research Core Unit Genomics
Street address Carl-Neuberg-Str. 1
City Hannover
ZIP/Postal code 30625
Country Germany
 
Platform ID GPL2881
Series (2)
GSE17344 Analysis of spatial mRNA expression differences in the skin of Casp-8F/–K5-Cre or Casp-8F/+K5-Cre mice
GSE17365 Analysis of mRNA expression differences in the skin of Casp-8F/–K5-Cre and Casp-8F/+K5-Cre mice

Data table header descriptions
ID_REF
VALUE log ratio (base 10) (rProcessedSignal / gProcessedSignal) (test / reference) (Casp-8F/-K5-Cre / Casp-8F/+K5-Cre) (ko / wt)

Data table
ID_REF VALUE
1
2
3 0.093762242
4 -0.192953594
5 -0.030962981
6 0.121161783
7
8 0.040904306
9 -0.087209386
10 0.003434686
11 -0.027827516
12 -0.029053143
13 -0.005872035
14
15 -0.029869908
16 0.010326017
17 -0.027616906
18 -0.068458623
19 -0.00680915
20 0.004278355

Total number of rows: 22575

Table truncated, full table size 377 Kbytes.




Supplementary file Size Download File type/resource
GSM433650_M1330-c3-35.txt.gz 3.9 Mb (ftp)(http) TXT
GSM433650_M1330-c5-25.txt.gz 3.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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