MPD: Data set: Lyons1

Lyons1: Plasma lipids and susceptibility to gallstones in F2 progeny of DBA/2J x CAST/EiJ (2003)

References (chronological)

1. Lyons MA, Wittenburg H, Li R, Walsh KA, Churchill GA, Carey MC, Paigen B. Quantitative trait loci that determine lipoprotein cholesterol levels in DBA/2J and CAST/Ei inbred mice. J Lipid Res. 2003 May;44(5):953-67. Epub 2003 Feb 16. PubMed 12588951

2. Lyons MA, Wittenburg H, Li R, Walsh KA, Leonard MR, Korstanje R, Churchill GA, Carey MC, Paigen B. Lith6: a new QTL for cholesterol gallstones from an intercross of CAST/Ei and DBA/2J inbred mouse strains. J Lipid Res. 2003 Sep;44(9):1763-71. Epub 2003 Jun 16. PubMed 12810825

3. Li R, Lyons MA, Wittenburg H, Paigen B, Churchill GA. Combining data from multiple inbred line crosses improves the power and resolution of quantitative trait loci mapping. Genetics. 2005 Mar;169(3):1699-709. Epub 2005 Jan 16. PubMed 15654110 FullText

Lyons1 downloads
QTL projects have several available downloads.
Use the QTL Data Downloads button near the bottom of this page.

Ontology terms mapped to Lyons1 measures:

MA:0000356 gall bladder
MA:0000358 liver
MA:0002501 plasma
MA:0002513 bile
MP:0000180 abnormal circulating cholesterol level
MP:0000181 abnormal circulating LDL cholesterol level
MP:0000184 abnormal circulating HDL cholesterol level
MP:0004773 abnormal bile composition
MP:0004847 abnormal liver weight
VT:0000180 blood cholesterol amount
VT:0000181 blood LDL cholesterol amount
VT:0000184 blood HDL cholesterol amount
VT:0003402 liver mass
VT:0005084 gall bladder morphology trait

Investigators	M A Lyons Gary A Churchill The Jackson Laboratory, Bar Harbor, ME
Participants	Li R, Wittenburg H, Paigen B
Contact	Gary A Churchill gary.churchill@jax.org
Affiliated Center	QTL Archive
Acknowledgements	Funding provided by NIH DK51568, DK36588, DK52911, DK34854, CA34196, GM070683 and HL55001; and the American Physiological Society, American Liver Foundation, and Deutsche Forschungsgemeinschaft
Project type	QTL Archive data set
MPD identifiers	Lyons1 MPD:130
Data changelog	No updates/corrections. Initial release date: 01/2008.

An intercross of CAST/EiJ and DBA/2J was generated to identify cholesterol gallstone susceptibility loci. F2 progeny (males only) were administered a high-fat (15%) diet for 10 wks and examined for gallstone formation and related phenotypes. Gallstones were characterized qualitatively and quantitatively, and lipid profiles determined for plasma samples. Mice were fasted prior to sample collection. For detailed protocols see associated publications (below).

QTL data set parameters:

Progenitor strains	CAST/EiJ DBA/2J
Cross direction notation	(CASTxDBA2) F1 x (CASTxDBA2) F1; (DBA2xCAST) F1 x (DBA2xCAST) F1
Cross type	F2 intercross
Population size	0 ♀ 278 ♂
Age	16-18wks

Measured phenotypes: To access these data use the QTL Data Downloads button at bottom of page.

Data set	Procedure / Protocol	Treatment	Phenotype Measure / Variable (click to view)	Panel	Sex	Age	Sample Size (Avg)
Lyons1	organ weights	high-fat diet	liver weight [g] liver_wt 13001	QTL population	m	16-18wks	N=278

Lyons1	histopathology	high-fat diet	gallstones, presence (score 0=absent, 1=present) [score] gallstone_presence 13002	QTL population	m	16-18wks	N=278

Lyons1	histopathology	high-fat diet	gallstones, screening (score 0=absent, 1=present, 2=solid gallstones) [score] gallstone_score 13003	QTL population	m	16-18wks	N=278

Lyons1	histopathology	high-fat diet	number of gallstones [n] gallstone_count 13004	QTL population	m	16-18wks	N=278

Lyons1	histopathology	high-fat diet	weight of gallstones [mg] gallstone_weight 13005	QTL population	m	16-18wks	N=278

Lyons1	histopathology	high-fat diet	sandy gallstones (score 0=absence, 1-4=severity) [score] gallstone_sandy 13006	QTL population	m	16-18wks	N=278

Lyons1	histopathology	high-fat diet	solid gallstones (score 0=absence, 1-4=severity) [score] gallstone_solid 13007	QTL population	m	16-18wks	N=278

Lyons1	histopathology	high-fat diet	cholesterol monohydrate crystals, aggregates (score 0=absence, 1-4=severity) [score] ChMC_agg 13008	QTL population	m	16-18wks	N=278

Lyons1	histopathology	high-fat diet	cholesterol monohydrate crystals (score 0=absence, 1-4=severity) [score] ChMC_ind 13009	QTL population	m	16-18wks	N=278

Lyons1	lipid profile	high-fat diet	total cholesterol (plasma) [mg/dL] chol 13010	QTL population	m	16-18wks	N=278

Lyons1	lipid profile	high-fat diet	HDL (plasma), log transformed [log(mg/dL)] HDL_log 13011	QTL population	m	16-18wks	N=278

Lyons1	lipid profile	high-fat diet	nonHDL (plasma) [mg/dL] nonHDL 13012	QTL population	m	16-18wks	N=278

To see more rows use the paging control at top.

Associated genomic features

MGI-curated QTL / genomic features that have been associated with this data set:
Chol6 Hdl1 Hdlq10 Hdlq11 Hdlq12 Lith1 Lith10 Lith11 Lith24 Lith6

Project / data set: Lyons1 a.k.a. Lyons_2003
Excel file: Data_Description_CASTxDBA_Lyons2003.xlsx
Excel file: ._Data_Description_CASTx129_Lyons2003.xlsx
Excel file: Data_Description_CASTx129_Lyons2003b.xlsx
CSV file: Lyons2003_CASTxDBA_B37_Data.csv
CSV file: ._Lyons2003_CASTx129_B37_Data.csv
CSV file: Lyons2003b_CASTx129_B37_Data.csv
Readme / text file: readme_Lyons2003.txt
Readme / text file: ._readme.txt
Readme / text file: readme_Lyons2003b.txt
QC plots, figures, etc.: QCReport_Lyons2003.pdf
QC plots, figures, etc.: QCReport_Lyons2003b.pdf