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Previous IMPC Data Release 11.0 Notes

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IMPC

  • Release: 11.0
  • Published: 23-February-2020

Statistical Package

  • PhenStat
  • Version: 2.20.3

Genome Assembly

  • Mus musculus
  • Version: GRCm38

Summary

  • Number of phenotyped genes: 6,440
  • Number of phenotyped mutant lines: 6,900
  • Number of phenotype calls: 75,844

Data access

  • Ftp interface: ftp
  • RESTful interfaces: APIs

Highlights

Data release 11.0

Release notes: Represents a major data release. This release includes:
  • First release to include data from the late adult pipeline.
  • Nearly 60 million datapoints and 590 thousand images.
  • Inclusion of data from the Czech Centre for Phenogenomics group.
  • Change the method of associating background strain to a colony, required for alignment for some colonies to corresponding control group.

Data Reports

Total Number of Lines and Specimens in DR 11.0

Phenotyping Center Mutant Lines Baseline Mice Mutant Mice
JAX 1,231 9,257 34,736
TCP 604 7,506 25,501
HMGU 346 3,605 6,404
CCP-IMG 91 1,293 1,524
KMPC 49 1,295 1,758
MARC 232 1,877 3,776
MRC Harwell 679 6,780 16,321
RBRC 99 2,097 1,939
ICS 237 2,518 3,828
WTSI 1,432 4,981 17,542
BCM 654 5,549 19,282
UC Davis 1,246 5,003 25,202

Experimental Data and Quality Checks

Data Type QC passed QC failed issues
categorical 17,290,216 3,167 * 69,876 *
unidimensional 12,660,671 56,530 * 342,796 *
time series 15,043,961 2,660 * 17 *
text 239,514 10,921 * 122,064 *
image record 519,670 0 0

* Excluded from statistical analysis.

Distribution of Phenotype Annotations

Created with Highcharts 8.2.0Number 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 phenotypepigmentation phenotyperenal/urinary system phenotypereproductive system phenotyperespiratory system phenotypeskeleton phenotypevision/eye phenotypeliver/biliary system phenotypemammalian phenotype01k2k3k4k5k6k7k8k9k

Production Status

Overall

Created with Highcharts 8.2.0Number of genesChart context menuGenotyping Status303042425 8405 8403 5213 521Micro-injection in progressChimeras obtainedGenotype confirmedCre Excision Complete02k4k6k8k
Created with Highcharts 8.2.0Number of genesChart context menuPhenotyping Status6866865985987 0877 087Phenotype Attempt RegisteredPhenotyping StartedPhenotyping Complete02.5k5k7.5k

By Center

Created with Highcharts 8.2.0Number 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 8.2.0Number 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 iMits.

Phenotype Associations

Created with Highcharts 8.2.0Number of phenotype callsChart context menuPhenotype calls per procedureCenter by centerJAXTCPHMGUCCP-IMGKMPCMARCMRC HarwellRBRCICSWTSIBCMUC DavisBCM_CSD_001IMPC_ACS_003IMPC_CBC_003IMPC_DXA_001IMPC_ECH_001IMPC_FER_001IMPC_HEM_002IMPC_IPG_001IMPC_OWT_001IMPC_XRY_001CCP_XRY_001IMPC_EYE_002IMPC_CBC_002IMPC_ECG_001IMPC_INS_003ICS_ROT_001IMPC_ACS_002IMPC_HEM_001JAXLA_CSD_001JAXLA_ECG_001JAXLA_GRS_001JAXLA_HEM_002JAXLA_LDT_001JAX_ECT_001JAX_LDT_001JAX_ROT_001JAX_TLS_001KMPCLA_CBC_003KMPCLA_DXA_001KMPCLA_HWT_001KMPCLA_XRY_001HRWLLA_CBC_002HRWLLA_DXA_001HRWLLA_EYE_001HRWLLA_OFD_001HRWLLA_XRY_001IMPC_ABR_001IMPC_LDT_001TCPIP_GRS_001TCPLA_CSD_003TCPLA_EYE_002TCPLA_HEM_002TCP_CHL_003IMPC_CBC_001MGP_IPG_001MGP_XRY_0010500100015002000250030003500400045005000
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Trends

Created with Highcharts 8.2.0Genes/Mutant LinesPhenotype CallsChart context menuGenes/Mutant Lines/MP CallsRelease by ReleasePhenotyped genesPhenotyped linesMP calls1.01.12.03.03.13.23.33.44.04.24.35.06.06.17.08.09.19.210.010.111.002000400060008000020000400006000080000
Created with Highcharts 8.2.0Data pointsChart context menuData pointsCategorical (QC failed)Categorical (QC passed)Categorical (issues)Image record (QC failed)Image record (QC passed)Image record (issues)Text (QC failed)Text (QC passed)Text (issues)Time series (QC failed)Time series (QC passed)Time series (issues)Unidimensional (QC failed)Unidimensional (QC passed)Unidimensional (issues)1.01.12.03.03.13.23.33.44.04.24.35.06.06.17.08.09.19.210.010.111.005000000100000001500000020000000
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