GEAM Rigor and Reproducibility Statement
Prior research & starting materials: GEAM uses reliable sources for starting materials. For example, when possible, GEAM uses Jackson Laboratory for mice and ATCC or Millipore-Sigma for cell lines. Starting materials from other laboratories are confirmed with PCR or STR profiling. Animals are maintained at AAALAC and NIH specific pathogen free (SPF) standards. GEAM employs a customer relations module to comprehensively capture all relevant details arising from discussions between GEAM staff and users to initiate and continue projects.
Experimental design & biological variables: GEAM adheres to strict SOPs in all animal handling and molecular biology procedures that meet or exceed industry-standard validation and quality control measurements. For example, all genome edited models are routinely characterized by targeted, ultra deep sequencing. For cells, a second confirmation sequencing of clones is performed before distribution. For animals, all founders (F0s) are outcrossed and progeny (F1s) are similarly sequenced in-house to mitigate unexpected issues with mosaicism.
GEAM uses automation where possible to ensure rigorous quality control standards. For example, cryogenically preserved samples are carefully tracked using a user-accessible database and monitored by automated sensor systems. Automated systems also ensure single-cell clonality and minimize human error by utilizing liquid handlers for library preparation and cherry-picking. Colony management software is used to unambiguously track animals and record history.
Authentication: GEAM uses careful methods and internal tracking systems to authenticate its data and deliverables. All sequencing data and project summary reports are made available to users. GEAM has developed a long-read sequencing “allele authentication” service to validate unanticipated, incorrect alleles that often go unnoticed by other groups. GEAM uses STR profiling to validate cell lines.