NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM306715 Query DataSets for GSM306715
Status Public on Mar 22, 2009
Title Mdr2 KO HCV transgene tumorous tissues sample 5
Sample type RNA
 
Source name Mdr2 KO HCV transgene tumorous tissues
Organism Mus musculus
Characteristics Mdr2 KO
HCV transgene
tumorous tissues
sample 5
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.
 
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 GPL6193
Series (2)
GSE12184 Exon 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
4304920 1.6577751636505
4304921 1.6657906770706
4304922 3.6509490013123
4304923 5.8382277488708
4304925 6.5742425918579
4304927 1.8857853412628
4304928 11.560699462891
4304929 9.8180932998657
4304930 2.1550571918488
4304931 2.7633981704712
4304932 2.9049725532532
4304933 2.6501295566559
4304934 2.0522789955139
4304935 4.1459364891052
4304937 0.87588107585907
4304938 3.4719097614288
4304939 1.4384453296661
4304940 2.5892078876495
4304941 4.7439231872559
4304942 7.2581243515015

Total number of rows: 1230714

Table truncated, full table size 28786 Kbytes.




Supplementary file Size Download File type/resource
GSM306715_D15Exon.CEL 63.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap