|
| Status |
Public on Sep 22, 2009 |
| Title |
liver_M_SPF_2_9 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mouse liver tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
growth protocol: specific pathogen free
|
| Treatment protocol |
Direct comparison between germ-free and specific pathogen free mice without treatment
|
| Growth protocol |
Adult NMRI mice were reared germ-free or specific pathogen free
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of tissue samples were extracted using RNAeasy mini kit (Qiagen) according to the manufacturers instructions.
|
| Label |
Cy3, Cy5
|
| Label protocol |
For fluorescence labeling, 3 µg of total RNA from the reference or experimental samples were amplified using Ambion Amino Allyl MessageAmp aRNA Kit (Anbion) and reverse transcribed in the presence of Cy5-dUTP (Amersham Inc.). Labeled aRNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
|
| |
|
| Channel 2 |
| Source name |
Universal mouse reference RNA (Stratagene CAT#740100-41, LOT#0610751)
|
| Organism |
Mus musculus |
| Characteristics |
sample: Universal mouse reference RNA
|
| Treatment protocol |
Direct comparison between germ-free and specific pathogen free mice without treatment
|
| Growth protocol |
Adult NMRI mice were reared germ-free or specific pathogen free
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of tissue samples were extracted using RNAeasy mini kit (Qiagen) according to the manufacturers instructions.
|
| Label |
Cy3, Cy5
|
| Label protocol |
For fluorescence labeling, 3 µg of total RNA from the reference or experimental samples were amplified using Ambion Amino Allyl MessageAmp aRNA Kit (Anbion) and reverse transcribed in the presence of Cy5-dUTP (Amersham Inc.). Labeled aRNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
|
| |
|
| |
| Hybridization protocol |
Labeled cDNA were re-suspended in DIG EasyHyb (Roche, Switzerland) buffer and hybridized overnight (14-16h) in the MAUI Hybridization chamber (BioMicro, USA).
|
| Scan protocol |
The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 6.1 image analysis software (Axon Instruments, USA).
|
| Description |
n/a
|
| Data processing |
The data were Lowess normalized. Normalized ratio of means defined by CH1/CH2
|
| |
|
| Submission date |
Feb 03, 2009 |
| Last update date |
Sep 22, 2009 |
| Contact name |
Martin Lloyd Hibberd |
| E-mail(s) |
hibberdml@gis.a-star.edu.sg
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60 Biopolis Street, #02-01, Genome
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL8146 |
| Series (1) |
| GSE14689 |
Gut microbiota regulate xenobiotic metabolism in the liver |
|
