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Sample GSM306682 Query DataSets for GSM306682
Status Public on Mar 22, 2009
Title Mdr2 +/- HCV transgene non tumorous liver tissues sample 4
Sample type RNA
 
Source name Mdr2 +/- HCV transgene non tumorous liver tissues
Organism Mus musculus
Characteristics Mdr2 +/-
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
 
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.
 
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

Data table header descriptions
ID_REF
VALUE Expression values calculated with RMA algorithm

Data table
ID_REF VALUE
4405834 8.9990425109863
5165333 9.0734586715698
5165438 7.3471155166626
4735792 4.7760863304138
5385541 4.8803143501282
5275881 5.5512666702271
5056341 6.2649631500244
5615807 11.019050598145
4626698 9.1411037445068
4516854 7.884792804718
4626795 3.5018262863159
5615976 6.9405336380005
4397098 7.7982144355774
5056665 6.7568755149841
4517241 4.0759224891663
4736988 5.0802450180054
5386563 8.9956130981445
5277090 8.6355180740356
4407824 9.4937219619751
5387258 6.7208580970764

Total number of rows: 95590

Table truncated, full table size 2233 Kbytes.




Supplementary file Size Download File type/resource
GSM306682_D13Exon.CEL 63.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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