|
| Status |
Public on Aug 20, 2008 |
| Title |
Abcb4_9weeks_UDCA_3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Abcb4 (+/+) liver
|
| Organism |
Mus musculus |
| Characteristics |
FVB/NJ mouse liver 9 weeks (wild type)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After sacrifice, livers were excised and divided in two parts; one part snap-frozen in liquid nitrogen for RNA isolation and one part in formalin for histology. RNA was isolated using the RNeasy mini Kit (Qiagen, Valencia, Ca, USA). The quantity of RNA was measured on a nano-drop spectrophotometer and the quality checked on an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, Ca, USA).
|
| Label |
Cy3
|
| Label protocol |
All samples were hybridized according to the Agilent’s protocol. Agilent’s Whole Mouse Genome Microarray Kit, 4 x 44K (G4122F)
|
| |
|
| Channel 2 |
| Source name |
Abcb4 (-/-) UDCA 9 weeks
|
| Organism |
Mus musculus |
| Characteristics |
FVB.129P2-Abcb4tm1Bor/J. Abcb4 (-/-) mouse liver UDCA feeding 9 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After sacrifice, livers were excised and divided in two parts; one part snap-frozen in liquid nitrogen for RNA isolation and one part in formalin for histology. RNA was isolated using the RNeasy mini Kit (Qiagen, Valencia, Ca, USA). The quantity of RNA was measured on a nano-drop spectrophotometer and the quality checked on an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, Ca, USA).
|
| Label |
Cy5
|
| Label protocol |
All samples were hybridized according to the Agilent’s protocol. Agilent’s Whole Mouse Genome Microarray Kit, 4 x 44K (G4122F)
|
| |
|
| |
| Hybridization protocol |
All samples were hybridized according to the Agilent’s protocol. Agilent’s Whole Mouse Genome Microarray Kit, 4 x 44K (G4122F)
|
| Scan protocol |
Scanning was performed on a GenePix 4000B microarray scanner (Molecular Devices, Sunnyvale, CA, USA).
|
| Description |
For feature finding, identification and quality control the Feature Extraction Software (Version 9.5.3) from Agilent was used.
|
| Data processing |
As measures of spot intensities we used the median of the foreground pixel intensities. To retain spots with more than half of the pixels in saturation, additional lower scans were made and saturated intensities modified. Differential transcription, measured as ratio in transcription between knockout and control, was estimated for each gene fitting a log-linear mixed effect model according to Kerr [10], including parameters for dye, array and gene, together with the gene-specific effects on dye, array and mouse type (knockout/control). The latter effect is the parameter of main concern as it represents the knockout effect on gene transcription for each gene (measured in log2 scale). Parameter estimates were obtained using the MicroArray ANOVA (MAANOVA) package by Wu et al. for the statistical language R. A threshold of significance of at least two-fold change together with a p<0.01 was chosen.
|
| |
|
| Submission date |
May 20, 2008 |
| Last update date |
May 27, 2008 |
| Contact name |
Esten Nakken |
| E-mail(s) |
esten.nakken@medisin.uio.no, stale.nygard@medisin.uio.no
|
| Organization name |
Institute for Experimental Medical Research
|
| Department |
Ulleval university Hospital
|
| Street address |
Kirkeveien 166
|
| City |
Oslo |
| ZIP/Postal code |
0407 |
| Country |
Norway |
| |
|
| Platform ID |
GPL4134 |
| Series (1) |
| GSE11507 |
Gene expression profiles of sclerosing cholangitis activity in mice |
|
