Studies from QTL Archive

A collection of QTL studies across populations and species, curated by the Churchill Group to form the QTL Archive ( Each study has phenotype and genotype data for members of a population derived from a specific cross, and includes a list of phenotypes, an Excel archive file and a .csv file formatted for use with R/qtl. Most pages include original analysis scripts and other files, and a list of associated MGI-curated genomic features. Users can locate a data set of interest, download the data, and reproduce or extend analyses locally using software such as R/qtl, J/qtl, QTLRel, or DOQTL. Marker locations use Cox build 37 coordinates unless otherwise stated. QTL Archive resource funded by NIH R01 grant GM070683 to Gary Churchill.

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Data set Procedure What's in this data set QTL cross Sex Age (weeks) Year
Ackerman1 ventilator
with methacholine
Lung, respiratory function, baseline and methacholine-challenged (several doses). airway resistance MCh A/J x C3H/HeJ backcross f 7-8wks 2005
Ankra-Badu1 colony observation, body size and weight, organ weights, fat pad weights Body, organ, fat pad weights, weight gain, litter size. subcutaneous, epididymal, liver, kidney, spleen, heart, testis, tail length, L6, M16i None M16i x L6 F2 intercross both 2-10wks 2009
Attie1 eQTL microarray eQTL study of obesity and type 2 diabetes using microarray. adipose, gastrocnemius muscle, hypothalamus, pancreatic islets, kidney, liver tissues None B6 x BTBR intercross. both 10wks 2015
Bailey1 open field test Open field test. Locomotor activity, anxiety-related behavior. None OFT C57BL/6J and C58/J both 8wks 2008
Bautz1 lipid profile, body weight Plasma lipids. Cholesterol, triglycerides. Nsdhl CHOL, TG I/LnJ both 12-14wks 2013
Beamer1 computed tomography Bone volume. None None C57BL/6J x CAST/EiJ intercross f 20wks 1999
Beamer2 biomechanical test, computed tomography, hormone quantification, DXA, body weight Bone morphology and strength, insulin-like growth factor 1. femur, trabecular spacing, peak maximum ultimate break load, stiffness IGF-1, IGF1, INS C57BL/6J x C3H/HeJ intercross F2 progeny f 16wks 2001
Bouma1 microscopy Fetal gonads microscopy study. Dax1 None Dax1 XY backcross m embryo 2005
Brich1 metabolite quantification Protein tau hyperphosphorylation. axonal microtubule stabilizing, Dab1 cytoplasmic adapter None BALB/cByJ x C57BL/6J intercross f 3wks 2003
Brockmann1 hormone quantification, colony observation, muscle weights, lipid profile, body weight, organ weights Body, organ weights, litter size, abdominal fat, lipids, insulin, leptin. Liver, kidney, muscle weights. Cholesterol, triglycerides, insulin-like growth factor, NMRI8, DU6i CHOL, INS, LEP, TG DBA2J x NMRI8 and DBA2J x DU6i intercrosses both 3-6wks 2009
Broman1 organ dimensions Gut length. Sox10, Sox10Dom None C3HeB/FeJ x C57BL/6J intercross both 2006
Bubier2 study archive Intestinal microbiome study. microbiota, flora, gut bacteria None CC pre both 2014
Burke1 body weight, biomechanical test, computed tomography Femur and vertebra morphology and strength. Monthly body weight 3 - 13 months. None BW (BALBxB6) F1 x (C3HxDBA/2) F1 f 14-56wks 2012
Chesler6 alcohol quantification, behavior observation, body weight, body temperature, rotarod
with ethanol
Sensitivity to ethanol. Baseline and ethanol. blood alcohol concentration, loss of righting reflex, rotarod, body temperature. EtOH C57BL/6J x 129S1/SvImJ both 9-34wks 2012
Clemens1 health assessment
with ultraviolet light
Immunosuppression of contact hypersensitivity after ultraviolet light exposure None UV BALB/cAnNCrl x C57BL/6NCrl backcross both 9-30wks 2000
Davidson1 health assessment Exencephaly, neural tube defects in embryos. None None BALB/cJ x FVB/NJ reciprocal backcross both embryo 2007
DiPetrillo3 organ weights, tail cuff Blood pressure (tail cuff), heart rate, heart weight. None BP, HR C3H x SWR intercross F2 progeny both 8wks 2004
Doorenbos1 urinalysis, body weight Urinalysis. Creatinine, microalbumin, body weight. kidney, Apoe Alb, BW, CREA, MA C57BL/6J_x_A/J_and_A/J_x_B6.Apoe-/-_intercrosses m 8-10wks 2008
Dorward1 histopathology Ovarian granulosa cell tumors histopathology. None None CAST/EiJ x SWXJ9/BmJ intercross f 8wks 2005
Dzur-Gejdosova1 organ weights, body weight, microscopy Sterility investigation. Sperm count, testes weight. None None PWD/Ph and C57BL/6J backcross m 9wks 2012
Farmer1 immune cell quantification, histopathology, microscopy, body weight, organ weights, health assessment, hormone quantification Colitis susceptibility, severity. Colon histopathology, body and spleen weight. cecum, proximal, distal, ulceration, diarrhea, fecal blood, interleukin 10 IL-10, IL-12, IL10, IL12 IL-10-deficient mice both 6wks 2001
Feng1 tail cuff, body weight, organ weights Blood pressure (tail cuff), kidney weight, body weight. None BP, BW 8 mouse intercross populations m 8wks 2009
Gatti2 complete blood count Whole blood neutrophil count and white cell count. None None DO population both 10-12wks 2014
Guay-Woodford1 histopathology, organ dimensions, body size and weight Kidney morphology, renal cystic disease severity. Bicc1jcpk None BALB/c-Bicc1jcpk-bpk x CAST/EiJ F2 progeny f 2wks 2000
Hageman1 urinalysis, eQTL microarray eQTL, urinary albumin excretion using microarray. creatinine. Alb, CREA MSxSM F2 intercross m 8-10wks 2011
Ishimori1 lipid profile, organ weights, histopathology, DXA, body weight, hormone quantification
with high-fat diet
Lipids, atherosclerosis lesions, parathyroid hormone after high-fat diet. None BMD, BMI, LW C57BL/6J x 129S1/SvImJ intercross f 20wks 2004
Jarvis1 fat pad weights Fat pad weight. Epistatic interactions. None None SM/J x LG/J advanced intercross both 13+wks 2011
Karst1 MRI, organ weights, metabolite quantification, pH assessment, colony observation, centrifugation, metabolic panel, body weight Characterization of high-muscle-mass mice. fat, lean, muscle mass, glucose, drip loss, carcass pH, glycogen, lactate, litter size, body weight, coat color, colorimetric assay BW, GLU BMMI816 x BMMI806 (Berlin Muscle Mouse) both 3-10wks 2011
Kiernan1 slit lamp, microscopy Ear microscopy (ampullae) and eye slit lamp study. Jag None Jag1 heterozygous mice f 2007
Kim1 metabolic panel, hormone quantification, fat pad weights, body weight Glucose, insulin, body and fat pad weights. None GLU, INS TallyHo and C57BL/6J backcross progeny m 20-26wks 2001
Kumar1 body weight, circadian wheel running, open field test
with cocaine
Open field test. Locomotor, anxiety-related, circadian behavior. Baseline and after cocaine i.p. None OFT C57BL/6J x C57BL/6N reduced complexity cross. both 10-14wks 2014
Leiter2 body weight, histopathology, health assessment, lipid profile, metabolic panel, DXA, hormone quantification Type 1 diabetes development study. diabetes score, age of onset, insulitis severity, body weight, bone mineral density, content, muscle, organ weights, glucose, insulin, leptin, fat, lean mass, cholesterol, HDL, fatty acids, triglycerides, colorimetric assay, H2g7, T1D BMD, BW, CHOL, FFA, GLU, INS, LEP, TG NOD x 129.H2g7 backcross. f 14-40wks 2009
Li1 histopathology, body weight, lipid profile
with western diet
Lipids, atherosclerosis lesion histopathology. High-fat, western-style diet. cholesterol, triglycerides, Apoe CHOL, TG C57BL/6 x C3H intercross f 12wks 2008
Lyons1 lipid profile, histopathology, organ weights
with high-fat diet
Lipids (plasma), liver weight, gallbladder and gallstone histopathology. monohydrate crystals, aggregates LW DBA/2J x CAST/EiJ F2 progeny m 16-18wks 2003
Lyons2 organ weights, lipid profile, organ dimensions, histopathology
with high-fat diet
Lipids (plasma), bile, liver weight, gallbladder and gallstone histopathology. None LW 129S1/SvImJ x CAST/EiJ F2 progeny m 16-18wks 2003
Lyons3 organ dimensions, histopathology, lipid profile
with high-fat diet
Lipids, gallbladder and gallstone histopathology after high-fat diet. cholesterol, HDL, triglycerides CHOL, TG 129S1/SvImJ x RIIIS/J F2 intercross m 14-20wks 2004
Maeda1 histopathology Atherosclerosis lesion histopathology, lesion sizes. None None None both 18-20wks 2017
Mahler1 histopathology, organ weights Colitis susceptibility. Colon histopathology, spleen weight. cecum, proximal, distal, ulceration, interleukin 10 IL-10, IL10 C3H/HeJBir x C57BL/6J backcrosses both 6wks 2002
Mathews1 histopathology Type 1 diabetes resistance. T1DM None ALR/Lt x NOD backcross f 8-40wks 2003
Moore1 study archive Gravitropic response in Arabidopsis. arabidopsis, thaliana None Ler x Cvi population both 2013
Mrug1 organ dimensions, body weight, histopathology, organ weights Kidney morphology. length, weight, volume None cpk mutant mice both 1-2wks 2005
Nishihara1 tail cuff Blood pressure (tail cuff). systolic, diastolic BP C3H x NZO and NZO x C3H intercross F2 progeny m 10wks 2007
Payseur1 body weight Body weight of Gough Island mice. None BW Gough Island mice x WSB intercross. both 1-16wks 2015
Payseur2 study archive Hybrid male sterility. Morphology, sperm count, histopathology. None None WSB/EiJ x PWD/PhJ intercross m 10-11wks 2018
Peters5 body weight, complete blood count Complete blood count measures on fetuses, newborns. red cell count, hemoglobin, hematocrit, corpuscular volume, concentration CBC, RBC, WBC, CHCM, HCT, HGB, MCH, MCHC C3H/HeJ+/wan x CAST/EiJ F2 progeny both fetus, newborn 2004
Pitman1 lipid profile
with high-fat diet
Cholesterol (plasma) after high-fat diet (several timepoints). None CHOL NZB/BlNJ x SM/J backcross progeny f 6-26wks 2002
Recla1 nociception assay Hot plate nociception. None HP DO population both 13-17wks 2013
Reifsnyder1 body weight, fat pad weights, metabolic panel, hormone quantification, lipid profile Body weight (several ages), fat mass, body mass index, fat pad weights. inguinal, peritoneal, mesenteric BMI, BW, GLU, INS, TG NZO/HlLtJ x NON/ShiLtJ backcross m 4-24wks 2000
Reifsnyder2 histopathology Type 2 diabetes onset. None None NOD x NOR intercross f 12-40wks 2005
Richards-Smith1 intake monitoring, body weight, metabolic panel, fat pad weights
with macronutrient diet option
Caloric intake, glucose, body and fat pad weights. Macronutrient diet option. retroperitoneal, epididymal, diet choice preference GLU C57BL/6J x CAST/EiJ F2 reciprocal crosses m 8-13wks 2002
Rodriguez1 in vitro assay Spleen, liver murine cytomegalovirus study. natural killer cell-mediated resistance, antiviral responses MCMV NZW x NZB F2 progeny both 8-12wks 2009
Sheehan1 urinalysis Urinalysis. Creatinine, microalbumin, body weight. None Alb, BW, CREA, MA C57BL/6J x DBA/2J intercross F2 progeny m 10wks 2007
Shimomura1 monitoring system Circadian activity. None None BALB/cJ x C57BL/6J F2 progeny both 2001
Solberg1 metabolic panel, organ weights, open field test, body weight, defensive burying task, forced swim test, hormone quantification Open field test, forced swim test, defensive burying task. None BW, GLU, INS, OFT WKY and Fisher 344 rat strain intercross both 11-17wks 2004
Stylianou1 body size and weight, fat pad weights, body weight
with high-fat diet
Body size, weight, fat pad weights after high-fat diet. adiposity index None SM/J x NZB/BlNJ F2 progeny both 24wks 2006
Stylianou2 body weight, lipid profile Lipids. Cholesterol, triglycerides, body weight. None BW, CHOL, TG B6.A consomic and F2 mouse crosses both 8-10wks 2006
Su2 histopathology, lipid profile, body size and weight
with high-fat diet
Lipids (plasma). Cholesterol, triglycerides, aortic lesions, body mass index. None BMI, CHOL, TG C57BL/6J x C3H/HeJ F2 intercross f 14wks 2009
Sugiyama2 tail cuff
with sodium chloride
Blood pressure (tail cuff) after sodium chloride intake. None BP, NaCl C57BL/6J x A/J reciprocal back crosses m 10wks 2001
Sugiyama3 organ weights, tail cuff, body weight Blood pressure (tail cuff), heart weight, body weight. None BP, BW BALB/cJ and CBA/CaJ F2 progeny m 10wks 2002
Sundberg2 histopathology Alopecia areata autoimmune disease susceptibility. None None C3H/HeJ x C57BL/6J intercross F2 progeny both 52wks 2003
Tsaih1 body weight, organ weights Brain weight, body weight. None BW inbred intercross (RIX) hybrids both 2005
Wang1 lipid profile, histopathology
with high-fat diet
Lipids (plasma). Cholesterol, inducibility, triglycerides, atherosclerosis lesions. None CHOL, TG C57BL/6J and NZB/BlNJ advanced intercross lines f 10-23wks 2003
Wergedal1 DXA, biomechanical test Bone mineral density, thickness, strength. peak maximum ultimate break load BMD NZB/BlNJ x RF/J F2 intercross f 10wks 2006
Wittenburg1 body weight, histopathology, organ dimensions, organ weights
with high-fat diet
Liver weight, gallbladder and gallstone histopathology. None LW AKR/J and SWR/J reciprocal backcrosses both 18-20wks 2002
Wittenburg2 organ dimensions, organ weights, body weight, lipid profile, histopathology
with high-fat diet
Lipids (plasma), liver weight, gallbladder and gallstone histopathology. None LW PERA/EiJ and I/LnJ reciprocal backcrosses both 6-16wks 2003
Wittenburg3 histopathology, lipid profile, body weight, organ dimensions, organ weights
with high-fat diet
Lipids (plasma), liver weight, gallbladder and gallstone histopathology. None LW DBA/2J and PERA/EiJ intercross both 2005
Xiong1 monitoring system Circadian behavior. None None C57BL/6J x 129S1/SvImJ backcross m 9-34wks 2011
Yi1 body weight, organ weights Body weight (several timepoints) and liver weight. M16I BW, LW M16i x CAST backcross both 2-12wks 2007
Yuan5 biomarker quantification Plasma levels of P-selectin and soluble vascular cell adhesion molecule-1. Apoe None apoE-/- f 18wks 2008
Zhang1 histopathology, hormone quantification, body weight, colony observation, lipid profile, metabolic panel
with western diet
Atherosclerosis and glucose homeostasis. Lesions, lipids, glucose, insulin. High-fat, western-style diet. apolipoprotein E-deficient mice, Apoe None C57BL/6 x BALB/cJ intercross f <6-18wks 2012