Comment[ArrayExpressAccession]	E-GEOD-37379
MAGE-TAB Version	1.1			
Public Release Date	2013-04-22
Investigation Title	Transcriptome analysis of the livers from mice that had been fed water-soluble extract of Pacific Krill			
Comment[Submitted Name]	Transcriptome analysis of the livers from mice that had been fed water-soluble extract of Pacific Krill
Experiment Description	Background: We previously reported that intake of a water-soluble extract of Pacific Krill (WEPAK) by mice decreases triglyceride accumulation in liver and suppresses weight gain induced by a high-fat diet.  However, the mechanisms mediating these phenomena were not investigated or revealed in our previous study.  Methods and Findings: Here, we investigated the effect of WEPAK in mouse liver using transcriptome analysis and discovered that WEPAK induced the expression of genes categorized into the gene ontology (GO) term lipid metabolic process.  Furthermore, two regulators of fatty acid β-oxidation, AMPK and PPARδ, were induced in the liver and muscle of mice that had taken in WEPAK.  Conclusions: These results indicate that WEPAK increased the expression of genes related to fatty acid β-oxidation via activation of AMPK and PPARδ.  WEPAK may have the effect of improving lipid metabolism and, therefore, may be beneficial in the prevention of obesity. Examination of 4 different feeding condtion (4mice/group)			
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl		
Person Last Name	Yamada	Yamada		
Person First Name	Hidetoshi	Hidetoshi		
Person Email	hyamada@ibrc.or.jp			
Person Affiliation	Iwate Biotechnology Reserch Center			
Person Address	Iwate Biotechnology Reserch Center, Narita 22-174-4, Kitakami-shi, Iwate, Japan			
Person Roles	submitter			
Protocol Name	P-GSE37379-4	P-GSE37379-1	P-GSE37379-3	P-GSE37379-2
Protocol Description	We used two original programs (kSusageA, kSusageB) witten in objective-C to analyze the Super SAGE data. The FASTAQ format fileswere split every 12,000,000 lines using Terminal. These files were processed to create FASTA format files using kSusageA. The kSusageA program extracts 26-base tags from reads of 35 bases, sorts the tags based on index sequence, and counts the frequency of the tags. The tags were compared to the NCBI mouse transcript database using BLAST. The reference sequence DNA IDs were picked from the results of BLAST analysis, and the tags were annotated using kSusageB. Supplementary_files_format_and_content: the frequency of the tags	The animals were randomly divided into four groups: normal diet (D12450B: Research Diets, Inc., New Brunswick, NJ, USA), normal diet with 1% WEPAK, high-fat diet (D12451: Research Diets, Inc.), and high-fat diet with 1% WEPAK (4 mice / group).	Total RNA was extracted from liver samples with an RNeasy lipid tissue kit. Double-stranded cDNA was synthesized with biotinated oligo-dT primer and the Double-Stranded cDNA Synthesis kit (Invitrogen) from 5 µg of total RNA. Double-stranded cDNAs were digested with NlaIII (New England Biolabs, Beverly, MA, USA) after being purified using a PCR purification kit (QIAGEN). Double-stranded cDNAs digested with NlaIII were bound to Dynabeads M270 streptavidin (Invitrogen). Adapter sequence 2 containing an EcoP15I restriction site was ligated to the double-stranded cDNAs that were bound to Dynabeads. Double-stranded cDNAs were digested with EcoP15I (New England Biolabs). Double-stranded cDNAs digested with EcoP15I and separated from Dynabeads were tag sequences. Adaptor sequence 1 that contained index sequence was ligated to tag sequences. Tag sequences were then amplified by PCR and gel purified.	Male C57BL/6 mice that were 4-weeks old (Charles River Laboratories, Tokyo, Japan) were housed in a temperature-controlled environment (23 ± 1°C) with a 12 h light/dark cycle.
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	FEEDING			
Experimental Factor Type	feeding			
Comment[SecondaryAccession]	GSE37379			
Comment[GEOReleaseDate]	2013-04-22			
Comment[ArrayExpressSubmissionDate]	2012-04-18			
Comment[GEOLastUpdateDate]	2013-04-22			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[AEExperimentType]	transcription profiling by SAGE			
Comment[AdditionalFile:Data1]	GSE37379_table_S2_processed.txt			
Comment[SecondaryAccession]	SRP012297			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR488594-SRR488609			
SDRF File	E-GEOD-37379.sdrf.txt