Previous IMPC Data Release 10.1 Notes

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IMPC

  • Release: 10.1
  • Published: 26 June 2019

Statistical Package

  • PhenStat
  • Version: 2.20.0

Genome Assembly

  • Mus musculus
  • Version: GRCm38

Summary

  • Number of phenotyped genes: 5,861
  • Number of phenotyped mutant lines: 6,255
  • Number of phenotype calls: 70,692

Data access

Highlights

Data release 10.1

Release notes: Represents a minor data release. Changes include:
  • Includes additional Acoustic Startle and Pre-pulse Inhibition (PPI) derived parameters for % Pre-pulse inhibition - Global. The formula was updated to relax derivation requirements. Specifically the update allows derivations to be calculated using 3 % PPI parameters rather than requiring all 4.
  • Updates to automated methods of detecting anomolous or missing data resulted in some extraneous datapoints being removed.
  • The embryonic day associated to Viability E14.5-E15.5 Secondary Screen was updated from E14.5 to E15.5
  • The process for generating genotype to phenotype associations for categorical parameters has been changed. A phenotpye call is made in the case where the data analysis for each individual sex is not significant, but analysis using the combined data from both sexes is significant.
  • Fixed issue analyzing Combined retina parameter resulting in more phenotype calls.

Data Reports

Lines and Specimens

Phenotyping Center Mutant Lines Baseline Mice Mutant Mice
JAX 1,226 8,413 35,252
TCP 546 7,104 24,892
HMGU 311 3,173 5,770
KMPC 43 869 1,067
MARC 232 1,877 3,776
MRC Harwell 596 5,893 15,626
RBRC 96 2,023 1,859
ICS 223 2,325 3,554
WTSI 1,329 4,540 21,316
BCM 597 4,572 17,476
UC Davis 1,056 4,156 23,749

Experimental Data and Quality Checks

Data Type QC passed QC failed issues
categorical 14,917,864 3,835 * 16,974 *
unidimensional 11,116,529 43,508 * 293,835 *
time series 13,444,019 2,615 * 11 *
text 192,175 11,124 * 45,751 *
image record 469,960 0 0

* Excluded from statistical analysis.

Distribution of Phenotype Annotations

Created with Highcharts 6.0.3Number of genotype-phenotype associationsChart context menuDistribution of Phenotype Associations in IMPChemizygoteheterozygotehomozygoteadipose 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 phenotypemortality/agingmuscle phenotypenervous system phenotyperenal/urinary system phenotypereproductive system phenotyperespiratory system phenotypeskeleton phenotypevision/eye phenotypeliver/biliary system phenotypemammalian phenotypepigmentation phenotype01k2k3k4k5k6k7k8k

Status

Overall

Created with Highcharts 6.0.3Number of genesChart context menuGenotyping Status313145455 0775 0773 5073 507Micro-injection in progressChimeras obtainedGenotype confirmedCre Excision Complete02k4k6k
Created with Highcharts 6.0.3Number of genesChart context menuPhenotyping Status8848846976976 1476 147Phenotype Attempt RegisteredPhenotyping StartedPhenotyping Complete02k4k6k8k

By Center

Created with Highcharts 6.0.3Number of GenesChart context menuGenotyping Status by CenterJAXTCPMonterotondoVETMEDUNIHarwellMonterotondo R&DSEATMARCOuluBCMCDTAHMGUCAM-SU GRCCCP-IMGCIPHECNBKMPCUCDICSWTSINARLabsRIKEN BRCMonashMicro-injection in progressChimeras obtainedGenotype confirmedCre Excision Complete01k2k3k4k5k6k
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Created with Highcharts 6.0.3Number of GenesChart context menuPhenotyping Status by CenterJAXTCPMonterotondoHarwellSEATMARCBCMCDTAHMGUCCP-IMGCIPHEKMPCUCDICSWTSIRIKEN BRCPhenotype Attempt RegisteredPhenotyping StartedPhenotyping Complete01k2k3k4k5k6k7k8k
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More charts and status information are available from iMits.

Phenotype Associations

Created with Highcharts 6.0.3Number of phenotype callsChart context menuPhenotype calls per procedureCenter by center88192193197111234115511359951091711121314151619360484112221233451266712881299202223242526282913037325213313437725613813993530313233343537383914326538614430126814878840444647151274276431552433159439714505152535657581651661672883264483286061636667453103997470717374757879189223103620105801098283845088687BCM_CSD_001BCM_OFD_001IMPC_ACS_003IMPC_CAL_003IMPC_CBC_003IMPC_CSD_003IMPC_DXA_001IMPC_ECG_002IMPC_ECH_001IMPC_EYE_001IMPC_FER_001IMPC_GRS_001IMPC_HEM_002IMPC_HWT_001IMPC_LDT_001IMPC_OFD_001IMPC_OWT_001IMPC_VIA_001IMPC_XRY_001IMPC_ABR_002IMPC_CBC_002IMPC_CSD_002IMPC_ECG_001IMPC_INS_002IMPC_IPG_001ICS_ROT_001IMPC_ACS_002IMPC_CSD_001IMPC_EYE_002IMPC_HEM_001IMPC_INS_003JAX_ECT_001JAX_HBD_001JAX_LDT_001JAX_PLC_001JAX_ROT_001JAX_SLW_001JAX_TLS_001JAX_URI_001HRWL_OWT_001IMPC_ABR_001IMPC_CAL_002IMPC_FEA_001TCP_CHL_003IMPC_CBC_001MGP_CSD_001MGP_IPG_001MGP_MTB_001MGP_XRY_0010200400600800100012001400