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Sample GSM75115 Query DataSets for GSM75115
Status Public on Sep 21, 2005
Title F2-ob/ob(B) 318
Sample type RNA
 
Source name Liver
Organism Mus musculus
Characteristics (C57BL/6J X BTBR) F2-ob/ob (leptin deficient) mice, Liver, 14 weeks, Gender = F, 4-hr fasting, MOE430A ArrayID = 318A100603, MOE430B ArrayID = 318B100703.
Extracted molecule total RNA
Extraction protocol Liver total RNA was extracted from frozen tissue samples with RNAzol reagent (Tel-Test, Inc.). Crude RNA samples were purified with RNeasy mini columns (Qiagen, Inc.) before being subjected to microarray studies. The RNA samples were processed according to the Affymetrix Expression Analysis Technical Manual. A total of 60 MOE430A and MOE430B arrays were used. Quantitative expression levels of all the transcripts were estimated using the RMA algorithm for normalization.
Label biotin.
Label protocol Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets according to Affymetrix Expression Analysis Technical Manual.
 
Hybridization protocol standard Affymetrix procedures
Scan protocol standard Affymetrix procedures
Description (C57BL/6J X BTBR) F2-318. We selected 60 (C57BL/6J X BTBR) F2-ob/ob mice based on the selective phenotyping algorithm (Jin et al. 2004). The 60 mice used in this study were a subset of F2 mice segregating for phenotypes associated with obesity and diabetes (Stoehr et al. 2000). The framework map consists of 145 microsatellite markers spanning the 19 mouse autosomes, with average spacing of 20 cM, augmented by markers in identified regions.
Data processing The data were processed with MAS5.0 to generate cell intensity files. Quantitative expression levels of all the transcripts were estimated using the RMA algorithm for normalization (Irizarry et al. 2003).
 
Submission date Sep 19, 2005
Last update date Sep 20, 2005
Contact name Alan D Attie
E-mail(s) attie@biochem.wisc.edu
Phone 608-262-4705
Fax 608-263-9609
URL http://www.biochem.wisc.edu/attie/
Organization name University of Wisconsin-Madison
Department Biochemistry
Lab Attie
Street address 433 Babcock Drive
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
Platform ID GPL340
Series (1)
GSE3330 Combined Expression Trait Correlations and Expression Quantitative Trait Locus Mapping

Data table header descriptions
ID_REF 318B100703
VALUE RMA values

Data table
ID_REF VALUE
1415670_at 7.86
1415671_at 9.1
1415672_at 9.09
1415673_at 4.32
1415674_a_at 7.59
1415675_at 7.92
1415676_a_at 10.14
1415677_at 8.9
1415678_at 9.61
1415679_at 9.79
1415680_at 8.13
1415681_at 8.55
1415682_at 6.99
1415683_at 8.92
1415684_at 7.57
1415685_at 6.33
1415686_at 8.48
1415687_a_at 10.36
1415688_at 9
1415689_s_at 7.49

Total number of rows: 22575

Table truncated, full table size 354 Kbytes.




Supplementary data files not provided

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