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Previous IMPC Data Release 12.0 Notes

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IMPC

  • Release: 12.0
  • Published: 13 September 2020

Statistical Package

Genome Assembly

Summary

  • Number of phenotyped genes: 7,022
  • Number of phenotyped mutant lines: 7,606
  • Number of phenotype calls: 98,621

Data access

  • Ftp interface: ftp
  • RESTful interfaces: APIs

Highlights

Data release 12.0

Release notes:

Represents a major data release. This release

  • Changes default statistical pipeline from PhenStat to OpenStats
  • Includes more sensitive detection for auditory brain stem response screen
  • More information about the statistical classification of results available
  • Better quality controlled late adult data

Data Reports

Total Number of Lines and Specimens in DR 12.0

Phenotyping Center Mutant Lines Baseline Mice Mutant Mice
TCP 631 7,720 25,940
JAX 1,597 10,526 42,694
HMGU 361 3,878 6,677
CCP-IMG 101 1,473 1,834
MRC Harwell 711 6,964 18,141
MARC 233 1,858 3,595
KMPC 53 1,385 1,841
RBRC 103 2,132 2,080
ICS 240 2,576 3,864
WTSI 1,540 5,109 17,864
UC Davis 1,325 6,482 29,721
BCM 711 6,060 20,299

Experimental Data and Quality Checks

Data Type QC Passed Data Points
categorical 19,587,640
image record 538,628
time series 16,917,206
ontological 1,142,459
text 383,858
unidimensional 14,377,881

* Excluded from statistical analysis.

Distribution of Phenotype Annotations

Created with Highcharts 8.2.2Number of genotype-phenotype associationsChart context menuDistribution of Phenotype Associations by Top-level MP Termhemizygoteheterozygotehomozygoteadipose tissue phenotypebehavior/neurological phenotypecardiovascular system phenotypecraniofacial phenotypedigestive/alimentary phenotypeembryo phenotypeendocrine/exocrine gland phenotypegrowth/size/body region phenotypehearing/vestibular/ear phenotypehematopoietic system phenotypehomeostasis/metabolism phenotypeimmune system phenotypeintegument phenotypelimbs/digits/tail phenotypeliver/biliary system phenotypemortality/agingmuscle phenotypenervous system phenotypepigmentation phenotyperenal/urinary system phenotypereproductive system phenotyperespiratory system phenotypeskeleton phenotypevision/eye phenotype01k2k3k4k5k6k7k8k9k

Production Status

Overall

Created with Highcharts 8.2.2Number of genesChart context menuGenotyping Status313142425 8605 8603 5213 521Micro-injection in progressChimeras obtainedGenotype confirmedCre Excision Complete02k4k6k8kGenotype confirmed5 860
Created with Highcharts 8.2.2Number of genesChart context menuPhenotyping Status5295297787787 0907 090Phenotype Attempt RegisteredPhenotyping StartedPhenotyping Complete02.5k5k7.5k

By Center

Created with Highcharts 8.2.2Number of GenesChart context menuGenotyping Status by CenterJAXTCPMonterotondoVETMEDUNIHarwellMonterotondo R&DSEATMARCOuluBCMCDTAHMGUCAM-SU GRCCCP-IMGCIPHECNBKMPCUCDICSWTSINARLabsRIKEN BRCMonashMicro-injection in progressChimeras obtainedGenotype confirmedCre Excision Complete01k2k3k4k5k6k7k
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Created with Highcharts 8.2.2Number of GenesChart context menuPhenotyping Status by CenterJAXTCPMonterotondoHarwellSEATMARCBCMCDTAHMGUCCP-IMGCIPHEKMPCUCDICSWTSIRIKEN BRCPhenotype Attempt RegisteredPhenotyping StartedPhenotyping Complete01k2k3k4k5k6k7k8k9k
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More charts and status information are available from our mouse tracking services iMits and GenTaR.

Phenotype Associations

Created with Highcharts 8.2.2Number of phenotype callsChart context menuNumber of Phenotype Calls by ProcedureFurther categorized by Embryo, Late Adult, and Early AdultEmbryoLate AdultEarly AdultGross Morphology Embryo E9.5Gross Morphology Placenta E9.5Viability E9.5 Secondary ScreenGross Morphology Embryo E12.5Gross Morphology Placenta E12.5Viability E12.5 Secondary ScreenGross Morphology Embryo E14.5-E15.5Gross Morphology Placenta E14.5-E15.5Viability E14.5-E15.5 Secondary ScreenGross Morphology Embryo E18.5Gross Morphology Placenta E18.5Viability E18.5 Secondary ScreenAcoustic Startle and Pre-pulse Inhibition (PPI)Auditory Brain Stem ResponseBody Composition (DEXA lean/fat)Challenge Whole Body PlethysmographyClinical ChemistryCombined SHIRPA and DysmorphologyCortical Bone MicroCTEchoElectrocardiogram (ECG)Electroconvulsive Threshold TestingEye MorphologyFear ConditioningFemoral MicroradiographyFertility of Homozygous Knock-out MiceGrip StrengthGross Pathology and Tissue CollectionHeart WeightHematologyHole-board ExplorationImmunophenotypingIndirect CalorimetryInsulin Blood LevelIntraperitoneal glucose tolerance test (IPGTT)Light-Dark TestLung mechanics by forced oscillationsOpen FieldOpen Field - centre startOrgan WeightPlasma ChemistryRotarodSleep WakeTail SuspensionThree-point BendTrabecular Bone MicroCTUrinalysisVertebral MicroradiographyViability Primary ScreenX-ray01k2k3k4k5k6k7k8k
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Trends

Created with Highcharts 8.2.2Genes/Mutant LinesPhenotype CallsChart context menuGenes/Mutant Lines/MP CallsBy Data ReleasePhenotyped genesPhenotyped linesMP calls1.01.12.03.03.13.23.33.44.04.24.35.06.06.17.08.09.19.210.010.111.012.002000400060008000030000600009000012000012.0● Phenotyped genes: 7 022 genes● Phenotyped lines: 7 606 lines● MP calls: 98 621 calls
Created with Highcharts 8.2.2Data PointsChart context menuData Points by Data ReleaseCategorical (QC passed)Image record (QC passed)ontological_datapoints_QC_passedText (QC passed)Time series (QC passed)Unidimensional (QC passed)1.01.12.03.03.13.23.33.44.04.24.35.06.06.17.08.09.19.210.010.111.012.005000000100000001500000020000000250000004.2● Categorical (QC passed): 6 431 595 ● Image record (QC passed): 208 924 ● ontological_datapoints_QC_passed: 0 ● Text (QC passed): 89 172 ● Time series (QC passed): 9 138 387 ● Unidimensional (QC passed): 4 797 248
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