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P ROGRAMS FOR G ENOMIC A PPLICATIONS. National Heart, Lung, and Blood Institutes National Institutes of Health. Mission Statement. To develop new resources, reagents, and education programs for investigators engaged in NHLBI-related research. PGA Mission. - PowerPoint PPT Presentation
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PROGRAMS FORGENOMICAPPLICATIONSNational Heart, Lung, and Blood InstitutesNational Institutes of Health
Mission StatementTo develop new resources, reagents, and education programs for investigators engaged in NHLBI-related research.
PGA MissionProvide new resources and reagents to link genes to biological function and make these readily available to the NHLBI community.
Facilitate workshops, courses, and visiting scientist programs to train investigators in the technologies being applied in the PGAs.
Rapidly disseminate data through the world wide web and public databases.
Organizational StructureCoordinating CommitteeBioinformaticsSubcommitteeProteomicsSubcommitteeData SharingSubcommitteeEducationSubcommitteeIntegrationSubcommitteeMicroarraySubcommitteePhenotypeSubcommittee
PGA ProgramsApplied Genomics in CardioPulmonary DiseaseJohns Hopkins University School of Medicine
Genomics of Cardiovascular Development, Adaptation, & RemodelingHarvard Medical School
Physiogenomics of Stressors in Derived Consomic RatsMedical College of Wisconsin
Genomics of Proteomics of Cell Injury and InflammationUniversity of Texas S.W. Medical Center
Innate Immunity in Heart, Lung, and Blood DiseasesThe University of Arizona
UW-FHCRC Variation Discovery ResourceUniversity of Washington
Mouse Models of Heart, Lung, and Blood DiseasesThe Jackson Laboratory
Expression Profiling of Rodent Models of Human DiseaseThe Institute for Genomics Research
Comparative Genomic Analysis of Cardiovascular GenesLawrence Berkeley National Laboratory
Genomic Analysis of Stress and InflammationHarvard Medical School
NHLBI Bay Area Functional Genomic ConsortiumThe David J. Gladstone Institute
SubcommitteeChairsBioinformaticsCarol Bult, Ph.D., The Jackson Laboratory
Data Sharing Isaac Kohane, M.D., Ph.D., Harvard Medical School
Education Scott Weiss, M.D., M.S., Harvard Medical School
Genomic Inventory/IntegrationEdward Rubin, M.D., Ph.D., The Lawrence Berkeley National Laboratory
MicroarrayJohn Quackenbush, Ph.D., The Institute for Genomics Research
PhenotypeAndrew Greene, Ph.D., Medical College of Wisconsin
ProteomicsThomas Kodadek, Ph.D., Univ. Texas S.W. Medical Center
Anticipated PGA Resources/ToolsMouse models of HLBS disorders
Rat models of HLBS disorders
Microarrays
DNA Variations (SNPs - locations, allele frequencies, genotypes and haplotypes)
Reagents (clones, antibodies, mice, and rats) Protocols
Bioinformatic Resources (software tools and databases)
BayGenomicsApply custom gene-trap vectors to inactivate genes in ES cells and to evaluate the functional importance of these in cardiopulmonary development and disease using computational approaches, expression profiling, in situ hybridization studies, and in select cases in animals. http://baygenomics.ucsf.eduPI: Dr. Stephen G. YoungFocus: Cardiopulmonary Development and Disease
CardioGenomicsTo link genes to function, dysfunction, and structural abnormalities of the cardiovascular system caused by clinically relevant genetic and environmental stimuli.
http://www.cardiogenomics.orgPI: Dr. Seigo IzumoFocus:Cardiovascular Development, Adaptation, andRemodeling
HopGenesTo identify the genes involved in tissue remodeling using expression profiling to explore the pathology of asthma, chronic obstructive pulmonary disease, cystic fibrosis, lung transplantation, acute lung injury, scleroderma, sarcoidosis, pulmonary hypertension, ischemic cardiomyopathy, and cardiac transplantation.http://www.hopkins-genomics.org PI: Dr. Joe G.N. GarciaFocus: Tissue Remodeling in Cardiopulmonary Disease
Innate ImmunityExplore genetic susceptibility in asthma, chronic obstructive pulmonary disease, myocardial infarction and deep venous thrombosis by evaluating polymorphisms in genes involved in innate immune responses.
http://innateimmunity.netPI: Dr. Fernando D. MartinezFocus: Genetics of HLB Disorders
JAX PGAApply a phenotype-driven approach to identify the genetic mechanisms underlying the physiology and pathophysiology of atherosclerosis, hypertension, lung function, blood formation, thrombosis, obesity, inflammation, and sleep function. http://pga.jax.orgPI: Dr. Luanne L. PetersFocus: Mouse Models of HLBS Disorders
PARABIOSYSTo identify and characterize the gene networks activated by pro-inflammatory, metabolic, and pathogenic stresses affecting cardiovascular and pulmonary systems. http://genetics.mgh.harvard.edu/Parabiosys/PI: Dr. Brian SeedFocus: Genetics of Inflammation and Stress
Berkeley PGAApply comparative genomics to identify and understand the role of cis-acting regulatory elements that affect the expression of cardiovascular genes. http://pga.lbl.govPI: Dr. Edward M. RubinFocus: Cardiovascular Gene Expression
PhysGenDissect multigenic common HLBS diseases through the development of panels of chromosomal substitution strains of rats (consomic rat panels).
http://pga.mcw.eduPI: Dr. Howard J. JacobsFocus: Rat Models of HLBS Disorders
Seattle SNPsTo identify variable sites in human genes to expand the resources available to explore the role of inter-individual variation and its relationship to disease risk, outcome and treatments for common human disorders. http://pga.mbt.washington.eduPI: Dr. Deborah A. NickersonFocus: Inflammation and Genetic Variability
SouthwesternElucidate the basic mechanisms underlying cell injury and inflammation through a combination of genomic and proteomic approaches. http://pga.swmed.eduPI: Dr. Stephen A. JohnstonFocus: Cell Injury and Inflammation
TREX
Explore gene-environment interactions using rodent models of human disease and cDNA microarray assays to elucidate patterns of gene expression in heart, lung, blood, and sleep disorders. http://pga.tigr.orgPI: Dr. John QuackenbushFocus: Gene Expression in HLBS Disorders
NHLBI PGA Research Network..........HopGenes - BaltimoreCardioGenomics - BostonPhysGen - MilwaukeeSouthwestern - DallasInnateImmunity- TucsonSeattleSNPs - SeattleJAX PGA - Bar HarborTREX - RockvilleBerkeley PGA- BerkeleyParaBioSys - BostonBayGenomics- San Francisco
NHLBI PGA Web Siteshttp://www.nhlbi.nih.gov/resources/pga/index.htmPROGRAMS FOR GENOMIC APPLICATIONS
PGA Web Sites (cont.)BayGenomics - http://baygenomics.ucsf.eduCardioGenomics - http://www.cardiogenomics.orgParaBioSys - http://genetics.mgh.harvard.edu/Parabiosys/JAX PGA - http://pga.jax.orgHopGenes - http://www.hopkins-genomics.orgInnateImmunity - http://innateimmunity.net
PGA Web Sites (cont.)Berkeley PGA - http://pga.lbl.govTREX - http://pga.tigr.orgPhysGen - http://pga.mcw.eduSouthwestern - http://pga.swmed.eduSeattleSNPs - http://pga.mbt.washington.edu
NHGRI/NHLBI
Howard JacobMCWMarco MarraUBCShaying ZhaoTIGRPeter TonellatoRat GDBCHOPieter de JongUniv UtahRobert WeissRAT GENOME SEQUENCING PROJECT
Goals
Produce a `draft sequence` of the genome,Assembly and first-pass annotation,Cross-species comparison,A public assembler,Foundation for a finishing effort,Interface with community,
Fold-Coverage Timelines (Year One)(Cumulative)All in MOU (with data release policy)
Time
BCM
Celera
GTC
Total
Q1
0.25/0.13
0.28/0
0.07/0.21
0.53
Q2
0.59
0.56
0.14
1.15
Q3
0.98
0.84
0.21
1.82
Q4
1.36
1.12
0.28
2.48
Strategy: Strain Selection:Howard Jacobs BN/SsNHsd
This Brown Norway strain has onlyseven heterozygous markers in themore than 4,000 tested i.e. it is very`isogenic` as a representative strain.
New BAC LibraryMade by Pieter de Jong from BN/SsNHsd female,
One enzyme so far~200 kb inserts10 X coverageSecond enzyme to come?
Doug Smith pursuing chr Y library,
Fingerprints:
UBC, ~40,000 for `de-randomization`~200,000 for f`print assembly,
BES:TIGR, ~200,000 paired ends
Strategy: BAC SkimsBAC skims to cover 90% of genomeOriginally 20,000 150 kb `de-randomized` BACs @ 1.0 x coverage,(384 reads per BAC) = 1 x clone coverage = 67% - 80% coverage~ 5,000 gaps for walks,Now 15,000 200 kb BACs @768 reads per BAC and 1.7 X coverage
Strategy: BAC Skims (cont`d)Reads in BACs:
2kb paired end (dye term) +++10kb paired end (dye term) --M13 (with primer chemistry) ?
Strategy: WGS Reads2kb paired end (dye term) +++10kb paired end (dye term) +++5kb and 50kb discussed,M13 (with primer chemistry) ?
- Usual- Assembly- Data `purity`Challenges:
Atlas:
A whole genome assembler
Lung StudieshypoxianormoxiaIsolated VesselResearch Services ComponentPhenotyping ComponentConditioning ProtocolGenomicsComponentProfilingRespiratoryStudiesBioinformatics ComponentConsomic Rat StrainsFunctionalMappingDNA & GenotypingDataBaseline & StressedExpression DataRatdistributionBaseline & StressedPhysiological DataGenomics ComponentGenotyping & Animal Production(Transponders and transfer)TIGR ConsomicExpression Data Expression low salthigh saltBlood Studies2,64015 strains/yr
330330330330330330330330
Mary Pat Kunert, RN, Ph.D., Project SupervisorMindy Dwinell, Ph.D. Project SupervisorMeredith Skelton, M.S. , Sr. Research AssociateJulie Messinger, M.S., Program Coordinator
Cardiac Studies:Jessica Laessig and William HutchinsRenal Studies:Larry Clowry and Mike Bregantini Biochemistry:Candace JonesLung Studies:Jess Powlas and Bernadette CabigasIsolated Vessel Studies:Janelle Yarina Respiratory Studies:Jenny Hogan and Andrea TrevettAnimal Delivery and Care: Alison KriegelLaboratory Support Services:Jennifer LabeckiPhenotyping Team
Co-investigators:Cardiac Studies:John Baker, M.D.Lung Studies:Christopher Dawson, Ph.D.Biochemistry Studies:Kirkwood Pritchard, Ph.D.Respiratory Studies:Hubert Forster, Ph.D.Isolated Vessel Studies:Julian Lombard, Ph.D.Vascular and Renal Studies:David Mattson, Ph.D. Richard Roman, Ph.DComponent Director - Allen W. Cowley, Jr, Ph.D.Phenotyping Component
P = 0.223
Treadmill Protocol (MAP)RestWalkRun5 minutes5 minutes5 minutes400l Blood draw @(3rd min.)400l Blood draw @(3rd min.)400l Blood draw @(3rd min.)Rectal
TempRectal
TempContinuous measurement of MAP & HR: Analyze Data from 30sec. before blood draws.
vascular
Rat Strain =HS-F
Wks of experiments =HS-M
VASCULAR PHENOTYPESRat 1Rat 2Rat 3Rat 4RAT 5RAT 6RAT 7RAT 8RAT 9RAT 10RAT 11RAT 12RAT 13RAT 14RAT 15RAT 16RAT 17RAT 18RAT 19RAT 20RAT 21RAT 22LS-F
HIGH SALT 4.0% (HS):HS-FHS-FHS-FHS-FHS-FHS-FHS-FHS-FHS-FHS-FHS-MHS-MHS-MHS-MHS-MHS-MHS-MHS-MHS-MHS-MLS-F/PSLS-M/PSLS-M
Constrictor response to Phenylephrine EC50
Constrictor response to Phenylephrine Log EC50
Dilator response to Acetycholine EC50
Dilator response to Acetycholine Log EC50
Dilator response to sodium nitroprusside EC50
Dilator response to sodium nitroprusside Log EC50
% Maximum Relaxation Acetylcholine
% Maximum Relaxation Sodium Nitroprusside
% Maximum Relaxation of Phenylephrine-Induced Contraction by 10% O2.
% Maximum Relaxation of Phenylephrine-Induced Contraction by 5% O2.
% Maximum Relaxation of Phenylephrine-Induced Contraction by 0% O2.
Fast slope of Phenylephrine-induced contraction
Slow slope of Phenylephrine-induced contraction
Maximum force (g) per wet weight of aorta (contraction)
Maximum force (g) per wet weight of aorta (relaxation)
RAT 23RAT 24RAT 25RAT 26RAT 27RAT 28RAT 29RAT 30RAT 31RAT 32RAT 33RAT 34RAT 35RAT 36RAT 37RAT 38RAT 39RAT 40RAT 41RAT 42RAT 43RAT 44
LOW SALT 0.4% (LS):LS-FLS-FLS-FLS-FLS-FLS-FLS-FLS-FLS-FLS-FLS-MLS-MLS-MLS-MLS-MLS-MLS-MLS-MLS-MLS-MLS-F/PSLS-M/PS
Constrictor response to Phenylephrine EC50
Constrictor response to Phenylephrine Log EC50
Dilator response to Acetycholine EC50
Dilator response to Acetycholine Log EC50
Dilator response to sodium nitroprusside EC50
Dilator response to sodium nitroprusside Log EC50
% Maximum Relaxation Acetylcholine
% Maximim Relaxation Sodium Nitroprusside
% Maximum Relaxation of Phenylephrine-Induced Contraction by 10% O2.
% Maximum Relaxation of Phenylephrine-Induced Contraction by 5% O2.
% Maximum Relaxation of Phenylephrine-Induced Contraction by 0% O2.
Fast slope of Phenylephrine-induced contraction
Slow slope of Phenylephrine-induced contraction
Maximum force (g) per wet weight of aorta (contraction)
Maximum force (g) per wet weight of aorta (relaxation)
&C&"Arial,Bold Italic"&16VASCULARPGA
Vascular.stats
Rat strain =
Wks of experiments =
VASCULAR PHENOTYPES
HIGH SALT 4.0% (HS):Mean (HS-T)Std Dev (HS-T)Std Error (HS-T)Max(HS-T)Min(HS-T)Mean (HS-F)Std Dev (HS-F)Std Error (HS-F)Max (HS-F)Min (HS-F)Mean (HS-M)Std Dev (HS-M)Std error (HS-M)Max (HS-M)Min (HS-M)
Constrictor response to Phenylephrine EC500.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
Constrictor response to Phenylephrine Log EC500.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
Dilator response to Acetycholine EC500.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
Dilator response to Acetycholine Log EC500.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
Dilator response to sodium nitroprusside EC500.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
Dilator response to sodium nitroprusside Log EC500.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
% Maximum Relaxation Acetylcholine0.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
% Maximum Relaxation Sodium Nitroprusside0.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
% Maximum Relaxation of Phenylephrine-Induced Contraction by 10% O2.0.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
% Maximum Relaxation of Phenylephrine-Induced Contraction by 5% O2.0.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
% Maximum Relaxation of Phenylephrine-Induced Contraction by 0% O2.0.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
Fast slope of Phenylephrine-induced contraction0.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
Slow slope of Phenylephrine-induced contraction0.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
Maximum force (g) per wet weight of aorta (contraction)0.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
Maximum force (g) per wet weight of aorta (relaxation)0.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+000.00E+0000.00E+000.00E+000.00E+00
LOW SALT 0.4% (LS):Mean (LS-T)Std Dev (LS-T)Std Error (LS-T)Max(LS-T)Min(LS-T)Mean (LS-F)Std Dev (LS-F)Std Error (LS-F)Max (LS-F)Min (LS-F)Mean (LS-M)Std Dev (LS-M)Std error (LS-M)Max (LS-M)Min (LS-M)
Constrictor response to Phenylephrine EC50000000000000000
Constrictor response to Phenylephrine Log EC50000000000000000
Dilator response to Acetycholine EC50000000000000000
Dilator response to Acetycholine Log EC50000000000000000
Dilator response to sodium nitroprusside EC50000000000000000
Dilator response to sodium nitroprusside Log EC50000000000000000
% Maximum Relaxation Acetylcholine000000000000000
% Maximim Relaxation Sodium Nitroprusside000000000000000
% Maximum Relaxation of Phenylephrine-Induced Contraction by 10% O2.000000000000000
% Maximum Relaxation of Phenylephrine-Induced Contraction by 5% O2.000000000000000
% Maximum Relaxation of Phenylephrine-Induced Contraction by 0% O2.000000000000000
Fast slope of Phenylephrine-induced contraction000000000000000
Slow slope of Phenylephrine-induced contraction000000000000000
Maximum force (g) per wet weight of aorta (contraction)000000000000000
Maximum force (g) per wet weight of aorta (relaxation)000000000000000
&C&"Arial,Bold"&12VascularStatistics
CX Response EC50
00
00
00
00
00
00
00
00
00
00
HS-F
HS-M
LS-F
LS-M
Constrictor Response to Phenylephrine EC50
Vascular PGA
CX Response LOG EC50
HS-F
HS-M
LS-F
LS-M
Constrictor Response to Phenylephrine Log EC50
Vascular PGA
DL Response ACH EC50
HS-F
HS-M
LS-F
LS-M
Dilator Response to Acetylcholine EC50
Vascular PGA
DL Response ACH Log EC50
HS-F
HS-M
LS-F
LS-M
Dilator Response to Acetylcholine EC50
Vascular PGA
DL Response SNP EC50
HS-F
HS-M
LS-F
LS-M
Dilator Response to SNP EC50
Vascular PGA
DL Response SNP Log EC50
HS-F
HS-M
LS-F
LS-M
Dilator Response to SNP Log EC50
Vascular PGA
% Maximum RX ACH
HS-F
HS-M
LS-F
LS-M
% Maximum Relaxation Acetylcholine
Vascular PGA
% Maximum RX SNP
HS-F
HS-M
LS-F
LS-M
% Maximum Relaxation Sodium Nitroprusside
Vascular PGA
% Maximum RX of PE CX by 10%O2
HS-F
HS-M
LS-F
LS-M
% Maximum Relaxation of Phenylephrine Induced Contraction by 10% O2
Vascular PGA
% Maximum RX of PE CX by 5% O2
HS-F
HS-M
LS-F
LS-M
% Maximum Relaxation of Phenylephrine Induced Contraction by 5% O2
Vascular PGA
% Maximum RX of PE CX by 0% O2
HS-F
HS-M
LS-F
LS-M
% Maximum Relaxation of Phenylephrine Induced Contraction by 0% O2
Vascular PGA
Maximum Force (CX Protocol)
HS-F
HS-M
LS-F
LS-M
Maximum Force (g)/wet weight of aorta (Contraction protocol)
Vascular PGA
Maximum Force (RX Protocol)
HS-F
HS-M
LS-F
LS-M
Maximum Force (g)/wet weight of aorta (Relaxation Protocol)
Vascular PGA
Means Phenotype #1
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
Constrictor Response to Phenylephrine EC50
Vascular PGA
Means Phenotype #2
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
Constrictor Response to Phenylephrine Log EC50
Vascular PGA
Means Phenotype #3
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
Dilator Response to Acetylcholine EC50
Vascular PGA
Means Phenotype #4
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
Dilator Response to Acetylcholine LogEC50
Vascular PGA
Means Phenotype #5
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (LS-M)
Mean (HS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
Dilator Response to Sodium Nitroprusside EC50
Vascular PGA
Means Phenotype #6
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
Dilator Response to Sodium Nitroprusside Log EC50
Vascular PGA
Means Phenotype #7
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
% Maximum Relaxation Acetylcholine
Vascular PGA
Means Phenotype #8
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
% Maximum Relaxation Sodium Nitroprusside
Vascular PGA
Means Phenotype #9
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
% Maximum Relaxation of Phenylephrine-induced Contraction to 10% O2
Vascular PGA
Means Phenotype #10
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
% Maximum Relaxation of Phenylephrine-induced Contraction to 5% O2
Vascular PGA
Means Phenotype #11
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
% Maximum Relaxation of Phenylephrine-induced Contraction to 0% O2
Vascular PGA
Means Phenotype #12
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
Maximum Force (g) per wet weight of aorta (Contraction protocol)
Vascular PGA
Means Phenotype #13
0000000000000
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Mean (HS-F)
Mean (LS-F)
Mean (HS-M)
Mean (LS-M)
Rat strain = Wks of experiments = VASCULAR PHENOTYPES
Mean (HS-T)
Mean (LS-T)
Maximum Force (g) per wet weight of aorta (Relaxation protocol)
Vascular PGA
* -p
Mean arterial pressure in SS and BN parentalrats and consomic chr. 13 and 16 on high salt (4.0%)
Chart1
2.22428571433.30214285710.50.7
1.579.3
9.311.834375
0.62.4
2.47583333335.7477777778
High Salt
Low Salt
PRA (ng/ml/hr)
SS
BN
SSBN13
FHH
SD
Sheet1
SSBNFHHSSBN13SD
SS rats1.0220.852.592.040.931.197.831.410.91.66.580.841.362.18681262360.5844502576HS PRA2.22428571430.61.570.59.30.70.62.47583333330.4
2.674.961.993.412.773.873.526.541.581.027.662.162.281.81.91730651850.5124217212
LS PRA3.30214285710.59.30.911.8343750.52.45.74777777780.8
FHH rats3.529.5512.4511.1413.039.398.328.3810.188.765.5711.8411.717.398.29.29533333332.599494090.6711864879Change is 1.8+/-0.3
10.1613.9713.213.4611.4611.748.7111.769.0813.116.112.5712.0111.9810.189.8711.8343751.9384047350.4846011837
SD rats1.961.91.750.310.8753.733.632.643.991.342.591.39131369140.4016376671
8.334.334.979.65.966.961.855.943.792.36377757930.7879258598
HS Protein excretion1.273.3400.8502.121.4801.92.42.76.782.11.901.7893333333
Sheet1
0.50.7
HS
LS
PRA (ng/ml/hr)
SD
FHH
SSBN13
BN
SS
Sheet2
Sheet3
Chart3
2.64111111118
18.913333333312
29.433333333325
31.111111111132
SS (females)
SSBN16 (females)
Angiotensin II (ng/kg/ml)
Change in MAP (mmHg)
50ng
25ng
10ng
5ng
Sheet1
SSBNFHHSSBN13SD
SS rats1.0220.852.592.040.931.197.831.410.91.66.580.841.362.18681262360.5844502576HS PRA2.22428571430.61.570.59.30.72.47583333330.4
2.674.961.993.412.773.873.526.541.581.027.662.162.281.81.91730651850.5124217212
LS PRA3.30214285710.59.30.911.8343750.55.74777777780.8
FHH rats3.529.5512.4511.1413.039.398.328.3810.188.765.5711.8411.717.398.29.29533333332.599494090.6711864879Change is 1.8+/-0.3
10.1613.9713.213.4611.4611.748.7111.769.0813.116.112.5712.0111.9810.189.8711.8343751.9384047350.4846011837
SD rats1.961.91.750.310.8753.733.632.643.991.342.591.39131369140.4016376671
8.334.334.979.65.966.961.855.943.792.36377757930.7879258598SD Protein excretion0.23642857140.13647243410.0364737922
BN Protein excretion19.210
SS Protein excretion1.273.3400.8502.121.4801.92.42.76.782.11.901.7893333333SS Protein excretion1.78933333331.68915152930.4222878823
SSBN13 Protein excretion5522
FHH Protein excretion13.12520.255.2516.27534.237.9523.587534.42559.62557.787531.3537.841.8520.92555.895.4SSBN16 Protein excretion
FHH Protein excretion32.6816.50852580054.1271314501
SD Protein excretion0.330.190.140.30.280.20.040.070.580.180.330.190.150.33
SSBN13 Protein excretion55+/-226.2-2.30.47161405.35.825
11142.32.5232503.510.1625
SSBN16 Protein excretion1217-4.47233201212.325
2321-2.71464901315.4125
BN Protein excretion19.2+/-10
SSBN16SDSS
5ng85.8252.6411111111
10ng1210.162518.9133333333
25ng2512.32529.4333333333
50ng3215.412531.1111111111
Sheet1
2.22428571433.30214285710.50.7
1.579.3
9.311.834375
2.47583333335.7477777778
HS
LS
PRA (ng/ml/hr)
SD
FHH
SSBN13
BN
SS
Sheet2
0.236428571419.21.78933333335532.68
Urinary Protein excretion (mg/24hrs)
SD
BN
SS
SSBN13
FHH
Sheet3
82.64111111115.825
1218.913333333310.1625
2529.433333333312.325
3231.111111111115.4125
SSBN16 (females)
SS (females)
SD (females)
Change in MAP (mmHg) to Ang II
50ng
25ng
10ng
5ng
82.64111111115.825
1218.913333333310.1625
2529.433333333312.325
3231.111111111115.4125
SSBN16 (females)
SS (females)
SD (females)
Change in MAP (mmHg) to Ang II
5ng
10ng
25ng
50ng
Chart4
3.6777777778-2
4.67777777781
17.3254.5
31.666666666712
SS (females)
SSBN16 (females)
Norepinephrine (g/kg/min)
Change in MAP (mmHg)
1.0
0.2
0.1
0.5
Sheet1
SSBNFHHSSBN13SD
SS rats1.0220.852.592.040.931.197.831.410.91.66.580.841.362.18681262360.5844502576HS PRA2.22428571430.61.570.59.30.72.47583333330.4
2.674.961.993.412.773.873.526.541.581.027.662.162.281.81.91730651850.5124217212
LS PRA3.30214285710.59.30.911.8343750.55.74777777780.8
FHH rats3.529.5512.4511.1413.039.398.328.3810.188.765.5711.8411.717.398.29.29533333332.599494090.6711864879Change is 1.8+/-0.3
10.1613.9713.213.4611.4611.748.7111.769.0813.116.112.5712.0111.9810.189.8711.8343751.9384047350.4846011837
SD rats1.961.91.750.310.8753.733.632.643.991.342.591.39131369140.4016376671
8.334.334.979.65.966.961.855.943.792.36377757930.7879258598SD Protein excretion0.23642857140.13647243410.0364737922
BN Protein excretion19.210
SS Protein excretion1.273.3400.8502.121.4801.92.42.76.782.11.901.7893333333SS Protein excretion1.78933333331.68915152930.4222878823
SSBN13 Protein excretion5522
FHH Protein excretion13.12520.255.2516.27534.237.9523.587534.42559.62557.787531.3537.841.8520.92555.895.4SSBN16 Protein excretion
FHH Protein excretion32.6816.50852580054.1271314501
SD Protein excretion0.330.190.140.30.280.20.040.070.580.180.330.190.150.33
SSBN13 Protein excretion55+/-22
SSBN16 Protein excretion
BN Protein excretion19.2+/-10
SSBN16SDSS
5ng8
10ng12
25ng25
50ng32
0.1-26.421253.6777777778
0.2121.3254.6777777778
0.54.512.37517.325
11215.287531.6666666667
-3.6-4.5335-1.53.74.1-0.7-2.43.6777777778
2.51.62.12.81.67.910.25.38.14.6777777778
12216202732182.617.32517.325
36302135404334182831.6666666667
Sheet1
000.50.7
00
00
00
00
HS
LS
PRA (ng/ml/hr)
SD
FHH
SSBN13
BN
SS
Sheet2
000000
Urinary Protein excretion (mg/24hrs)
SD
BN
SS
SSBN13
FHH
Sheet3
0
0
0
0
SSBN16 (females)
Change in MAP (mmHg) to Ang II
50ng
25ng
10ng
5ng
000
000
000
000
SD (females)
SS (females)
SSBN16 (females)
Norepinephrine (g/kg/min)
Change in MAP (mmHg)
Cardiac Conditioning and Phenotyping Protocol 8 week old rats
Sheet1
Conditioning Protocol (16-21 Days)Anesthesia and Heart Excision30 min perfusion25 min Global Ischemia40 min Reperfusion2 hours, 20 min Reperfusion
Pre-IschemicPost-Ischemic
Sheet2
Sheet3
Post ischemic infarct size (%)
Recovery developed ventricular pressure (%)
blood draw from carotid catheter in anesthetized rats following chronic exposure to hypoxia or normoxiaANP-15 (Marshfield Clinic)Small Animal Profile (ANP-1) Glucose, AST, ALT, Alkaline Phosphatase, Total Bilirubin, Total Cholesterol, Total Protein, Albumin, Urea Nitrogen, Creatinine, Phosphorus, Calcium, Sodium, Potassium, Chloride, Bicarbonate, Anion Gap Complete Blood Count With Differential (CBC)RBC, Hemoglobin, Hematocrit, MCV, MCH, MCHC, RDW, Platelet, WBC and DifferentialBiochemical Measurements
Lung StudieshypoxianormoxiaIsolated VesselResearch Services ComponentPhenotyping ComponentConditioning ProtocolGenomicsComponentProfilingRespiratoryStudiesBioinformatics ComponentConsomic Rat StrainsFunctionalMappingDNA & GenotypingDataBaseline & StressedExpression DataRatdistributionBaseline & StressedPhysiological DataGenomics ComponentGenotyping & Animal Production(Transponders and transfer)TIGR ConsomicExpression Data Expression low salthigh saltBlood Studies2,64015 strains/yr
330330330330330330330330
Airway Resistance at 100 ml/min/gm
PGA Respiratory Protocol TimelineMeasuring changes in Pulmonary Ventilation (VE), Tidal Volume (VT) and frequency (f) during Hypoxia (12% O2) and Hypercapnia (7% CO2).
Treadmill Studies
Treadmill Studies
Hyper-capniaStudy.Treadmill Adaptation & Data Analysis
Hypoxia Study
Treadmill& Box Adaptation with N2
Treadmill& Box Adaptation with CO2Treadmill& Box Adaptation Surgery Catheter Implantation in Femoral Artery
TreadmillAdaptationTreadmillAdaptation -11 week old rats Monday Tuesday Wednesday Thursday Friday
Week 1Pre-surgical ConditioningWeek 2Surgery &AdaptationWeek 3StudiesMeasuring Mean Arterial Pressure and Blood Gas Responses to ExerciseTreadmill Studies
11 week old ratsVascular Conditioning and Contraction Protocol
Vascular Conditioning and Relaxation Protocol 11 week old rats12:00 pm
Sheet1
Conditioning Protocol (16-21 Days)Pre-Surgical PreparationAnesthesia and Aorta ExcisionPost-Surgical PreparationInitial Pre-Conditioning ProceduresAcetylcholine RelaxationSodium Nitroprusside Relaxation
0.4% or 4% NaCl1 nM to 30 uM
Sheet2
Sheet3
Sheet1
Conditioning Protocol (16-21 Days)Pre-Surgical PreparationAnesthesia and Aorta ExcisionPost-Surgical PreparationInitial Pre-Conditioning ProceduresAchetylcholine RelaxationSodium Nitroprusside Relaxation
0.1 nM to 30 uM
Sheet2
Sheet3
Renal Cardiovascular Phenotyping Protocol
13 Weekold RatsWeek 1Week 2
Sheet1
Conditioning Protocol (16-21 Days)Surgical PreparationSurgical PreparationBase Line Pressure Recordings and urine Collection setupBase Line Pressure Recordings, Angiotensin II Dose Response Infusion, and Urine collectionBase Line Pressure Recordings and Norepinephrine Dose response Infusion
Monday Wk 1Tuesday Wk 1Wednesday Wk 1Thursday Wk 1Friday Wk 1
Sheet2
Sheet3
Sheet1
Base Line Recordings for High SaltBase Line Recordings for High Salt and Urine collection setupBase Line Recordings for High Salt Blood collection and Lasix InjectionLow Salt Urine collection setupBase Line Pressure Recordings, Urine collection, and Blood collection
Monday Wk 2Tuesday Wk 2Wednesday Wk 2Thursday Wk 2Friday Wk 2
Sheet2
Sheet3
Carotid catheter & Endotrachael TubeInsertionMethacholineChallengeHeart & Lung ExtractionP/Q Curve, MB+& FAPGG Experiments10 Week old ratsLung Prep TimelineMarshfield Blood Samples via catheter~25 minutes
Collect Data:ResistanceCompressionTidal VolumeBreathing FrequencyMinute VentilationExtract Lungs for PerfusionExtract Heart for RV & LV WeightsLiver Specimen for DNA ProcessingCollect Data:Change in Pressure w/ flowFAPGG AbsorbanceMB+ AbsorbanceLung Wet Weight~35 minutesAnesthetize RatPlace Rat in Plethysmograph & Insert Esophageal BalloonRemove Rat to SurgeryAttach Trachea & Pulmonary Artery to Perfusion ApparatusAnesthetize Next Rat
Revision 8
PhysGen PGA Phenotyping Production Schedule
(Color indicates phenotyping, black indicates conditioning, * indicates additional group)(Vascular group using nave animals; study starts wk 1 of 5 wks)
Date Wk 1 (Monday)RenalRespiratoryVascular High SaltVascular Low SaltLung HypoxiaLung NormoxiaCardiac HypoxiaCardiac NormoxiaComments
12/18/00SDSDSDSDSDSDSDRespiratory will do their SD group starting 2/5.
12/25/00SDSDSDSDSDSDSD2 weeks for hypoxia chamber modifications, repairs
1/1/01SDSDSDSDSDSDSD
1/8/01SDSD, SSSD,SSSDSDSDSDstart Vascular group for best age fit
1/15/01SD, SSSDSSSD, SSSSSD, SSSSSD, SSstart SS Cardiac, Lung, renal groups; Respiratory do SD group
1/22/01SSSDSSSSSSSSSSSS
1/29/01SSSD, SSSSSSSSSSSSSS
2/5/01SS, FHHSD, SSSS,FHHSS,FHHSS,FHHSS, FHHSS,FHHstart all groups but Respiratory and High Salt Vascular
2/12/01SS, FHHSD,SS,FHHSD*,FHHFHHSS,FHHFHHSS, FHHstart Respiratory group for best age fit; Vascular group study Low Salt SD group of females 2/12
2/19/01FHH, SS*SS,FHHSS-RenalFHHFHHFHHFHHFHH, SD*Vascular study on rats 2/19 after SS Renal study - for comparison
2/26/01FHH, SS*SS,FHHFHH, SD*FHHFHHFHHFHH, SD*Renal surgery 2/26 in 5th fl.lab
3/5/01FHH, SS*, 16FHH,SSBN16SS-Resp, SD*FHH, 16SS.BN16FHH, SD*, 16Downtime for hypoxia chamber maintenance w/o 3/5; Vascular study on 3/12 after SS Resp study
3/12/01SS*, 16FHH,SSBN16Progesterone-SD, SD*SSBN16,SD*SS.BN16SD*, SSBN16Phenotyper training 12th; Vascular group do progesterone study on SD 3/5; Renal surgery 5th fl.
3/19/01SS*, 16SS.BN16FHHSD*SSBN16,SD*SSBN16SD*, SSBN16Phenotyper training 19th
3/26/01SSBN16, SD*SS.BN16FHHSD*SSBN16,SD*SSBN16,SD*SS.BN16
4/2/01SSBN16, SD*SS.BN16FHH,SSBN16SSBN16SD*SSBN16,SD*SD*, 16*SSBN16,16*
4/9/01FHH,SSBN16SSBN16SD*, 16SD*, 16*SD*, 16*SSBN16*PGA-CC meeting in Milwaukee
4/16/01SSBN13SSBN16, 13SSBN16, 13SD*, 1616*SD*, 16*SSBN16*
4/23/01SSBN13SSBN13SSBN16, 13SSBN16, 13SD*, 16, 1316*, 1316*SSBN16*
4/30/01SSBN13SSBN13SS.BN 13SSBN16, 13SBN16, 1316*, 13SSBN16*holiday 5/28 Monday, affects week 5
5/7/01SSBN13SSBN13SS.BN 13SS.BN 13SSBN 1316*, 13SS.BN13SS.BN13holiday 5/28 Monday, affects week 4
5/14/0113, BN, 16*SSBN13, BNSSBN13SSBN13SSBN13SS.BN13SSBN13
5/21/01BN, 16*BNSSBN13SS.BN13SSBN13
5/28/01BN, 16*BNBNBNSSBN13SSBN13First data release June 1
6/4/01BN, 16*BNBNBNBNBNBNSSBN13, BNholiday 7/4 Wednesday, affects week 5
6/11/01BN, 16*BNBN, SSBN18BN,SSBN18BNBNBNBNMidwest Phys. Society meeting - Madison 6/11-12, holiday 7/4 Wednesday, affects week 4
6/18/01SSBN18BN, SSBN18BN,SSBN18BN,SSBN18BNBNBNDowntime for hypoxia chamber maintenance 6/18
6/25/01SS.BN18SS.BN18BN,SSBN18BN,SSBN18BN, SSBN18BN, SSBN18BN, SSBN18
7/2/01SS.BN18SSBN18SSBN18SS.BN18BN, SSBN18SS.BN18BN, SSBN18
7/9/01SS.BN18SS.BN18SSBN18SS.BN18SS.BN18SS.BN18SS.BN18
7/16/01SS.BN18SS.BN18SS.BN18SS.BN18SS.BN18Second data release September 7
7/23/01SS.BN18SS.BN18SS.BN18
7/30/01SS.BN18
8/6/01SS.BN18holiday 9/3 Monday, affects week 5
8/13/01holiday 9/3 Monday, affects week 4
8/20/01SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20
8/27/01SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20
9/3/01SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20SS.BN20
9/10/01SSBN20, 11SSBN20, 11SSBN20, 11SSBN20, 11SSBN20, 11SSBN20, 11SSBN20, 11SSBN20, 11
9/17/01SSBN20, 11SSBN20, 11SS.BN11SSBN20, 11SS.BN11SSBN20, 11SS.BN11SSBN20, 11Downtime for hypoxia chamber maintenance w/o 9/17
9/24/01SS.BN9SS.BN9SS.BN9SS.BN9SS.BN9SS.BN9SS.BN9SS.BN9
10/1/01
10/8/01
10/15/01SS.BN12SS.BN12SS.BN12SS.BN12SS.BN12SS.BN12SS.BN12SS.BN12Third data release December 7
10/22/01holiday 11/22 & 23 Thursday & Friday, affects week 5
10/29/01holiday 11/22 & 23 Thursday & Friday, affects week 4
11/5/01SS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNx
11/12/01
11/19/01SS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNx
11/26/01holiday 12/24 & 25 Monday & Tuesday, affects week 5
12/3/01holiday 12/24 & 25 Monday, Tuesday, affects week 4, holiday 1/1 Tuesday affects week 5
12/10/01holiday 1/1 Tuesday, affects week 4, downtime for hypoxia maintenance 12/10
12/17/01SS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNx
12/24/01
12/31/01
1/7/02SS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNxSS.BNx
Total Complete Calendar year 111 consomic, 4 parental
Total Complete in Grant year 1 (9/00-8/01)3 consomic, 4 parental
summary of 5 week protocol
week 1 - high salt diet renal and vascular
week 2 - hypoxia conditioning
week 3 - hypoxia conditioning; respiratory conditioning
week 4 - renal and respiratory surgery; all groups - studies
week 5 - all groups - studies
&LJ. Messinger&CPage &P of &N&R&D
Hypoxia & Hypercapnia Protocol(Ventilation and MAP)Put rat in box 20 Min.ControlInject gas N2 or CO2 Equil.
Stop Recording1st Rectal Temp 5 1 min. 2 & 3 min. 4,5 & 6 min. 7,8 & 9 2nd Rectal TempBlood draw 400l (Min. 3)Blooddraw 400l (Min 8)Calibration (30 Sec.)Calibration (30 Sec.)Analyze Data (H1) Analyze Data (H2)
PhysGen PGA production summary
RatsCardiacCardiacLungLungVascularVascularRenalRespiratory
HypoxicNormoxicHypoxicNormoxicHigh SaltLow SaltBiochem
BornWeanedAssignedCompleteStatusAssignedCompleteStatusAssignedCompleteStatusAssignedCompleteStatusAssignedCompleteStatusAssignedCompleteStatusAssignedCompleteStatusAssignedCompleteStatusStatus
SD10010010075501007050100001000010010050100100501007050100652550
SS100100100702510085251008025100902510010025100100251007925100732525
FHH100100100802510095251007525100802595100251001009025100832525
SSBN161001001009525100100100100100100100
SSBN137563
BN3825
SS.BN18April
SS.BN20June
SS.BN11July
SS.BN9July
SS.BN12Aug
Definitions:
Assigned = percentage of # assigned out of 20 possible (or 2 if the control), at transfer to phenotyping
Complete = percentage of # that generated data from phenotyping out of # assigned
Status: 0% = data not analyzed by phenotypers
25% = data completed by phenotypers
50% = data approved by Mary Pat and PI's (may result in a change to percent complete)
75% = data packaged by RSC
100% = data on the web
&CPGA Production Summary(%)
&LJ. Messinger&R&D