|
| Status |
Public on Mar 22, 2009 |
| Title |
Mdr2 +/- no HCV transgene non tumorous liver tissues sample 4 |
| Sample type |
RNA |
| |
|
| Source name |
Mdr2 +/- no HCV transgene non tumorous liver tissues
|
| Organism |
Mus musculus |
| Characteristics |
Mdr2 +/-
no HCV transgene
non tumorous liver tissues
sample 4
|
| Treatment protocol |
Non fasting mice were anesthetized with isoflurane and sacrificed by cervical dislocation. Livers were rapidly excised and weighed; part of the liver was fixed in 4% buffered formaldehyde for histological analysis, and the remaining tissue was rapidly frozen in liquid nitrogen and stored at -80ºC until use.
|
| Growth protocol |
Mice were maintained under specific pathogen-free conditions at the Specific Pathogen-Free (SPF) unit, Faculty of Medicine, Hebrew University, under a 12 h light/dark cycle, and provided with food and water ad libitum. The Institutional Animal Welfare Committee (NIH approval number OPRR-A01-5011) approved all animal experiments. All animal experiments were performed according to national regulations and institutional guidelines. Founders of the FVB.129P2-Abcb4tm1Bor (Mdr2-KO; old name FVB.129P2-Pgy24tm1Bor) mice were purchased from the Jackson Laboratory (Bar Harbor, USA) 11. Transgenic mice expressing the whole HCV 1b polyprotein were kindly provided by Prof. N. La Monica (IRBM, P. Angeletti, Pomezia, Italy) 9. Double Mdr2-KO/HCV-Tg mice were produced by crossing between homozygous Mdr2-KO and HCV-Tg mice, and by backcrosses of the resulting F1 hybrid (both Mdr2- and HCV-heterozygous) with the parental Mdr2-KO strain. Appearance of tumors was monitored by ultrasound from the age of 10 months, using an ATL 5000 device (ATL, Bothell, WA) with linear transducer (12-15 mHz). Mice were sacrificed at the age of 14 months, when tumor appearance was detected in most Mdr2-KO mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from snap frozen mouse liver tissues with the Trizol® reagent (Invitrogen, Carlsbad, CA) as described by the manufacturer.
|
| Label |
biotin
|
| Label protocol |
The sample labeling was performed according the Affymetrix protocols: http://www.affymetrix.com/support/technical/manual/expression_manual.affx
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| |
|
| Hybridization protocol |
The sample hybridization was performed according the Affymetrix protocols: http://www.affymetrix.com/support/technical/manual/expression_manual.affx
|
| Scan protocol |
The stained array was scanned on the Affymetrix scanner
|
| Description |
According to submitted paper: HCV tumor promoting effect is dependent on host genetic background
|
| Data processing |
The raw data were processed by the Partek® Genomics SuiteTM (Partek GS) (Partek Inc., St. Louis, MO) software. The “extended” subsets of probe-sets was used. RMA algorithm (Partek defaults) was applied for summarization, and the normalization was performed by the quantile method. The normalized expression values were processed by the Partek batch removing tool. Probe-set mean was applied for evaluation of transcript cluster expression level.
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| |
|
| Submission date |
Jul 21, 2008 |
| Last update date |
Jan 04, 2012 |
| Contact name |
Mark Katzenellenbogen |
| E-mail(s) |
markbogen@gmail.com
|
| Phone |
972-3-5317119
|
| Fax |
972-3-7384097
|
| Organization name |
Bar Ilan University
|
| Department |
THE FACULTY OF LIFE SCIENCE, BIOINFORMATICS AND MICROARRAY UNIT
|
| Street address |
Ramat-Gan 52900, Israel
|
| City |
Ramat-Gan |
| ZIP/Postal code |
52900 |
| Country |
Israel |
| |
|
| Platform ID |
GPL6096 |
| Series (2) |
| GSE12183 |
Transcript analysis of HCV tumor promoting effect |
| GSE12185 |
HCV tumor promoting effect is dependent on host genetic background |
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