Specific examples of different quality metrics based on different classes of data:
In vitro/cell-based chemical activity:
Quality Control Metrics: n=>3 data points per concentration; concentration coverage within 3 logs of EC50/IC50; data will include measures of central tendency (mean, median, mode, etc.) and measures of variability (SD, SEM, 95% CI, etc.)
Key Factors for Metadata: Cell line/vector information; assay conditions; instrumentation platform
Data Repositories: PDSP, PubChem, or other suitable repositories
Tracking Identifiers: DOI for weblink
Release Policy: Available immediately after QC metrics met (20% delayed until pre-print deposition in bioRxiv)
Mouse pharmacological activity:
Quality Control Metrics: n=>3 data points per dose; attempt at dose response; data will include measures of central tendency (mean, median, mode, etc.) and measures of variability (SD, SEM, 95% CI, etc.)
Key Factors for Metadata: Mouse line RRID#, in-house husbandry conditions, compound vehicle, etc.
Data Repositories: primary data in KOMP; knowledge summary in KMC
Tracking Identifiers: DOI for weblink
Release Policy: Available immediately after QC metrics met, (20% delayed until pre-print deposition in bioRxiv)
Mouse protein expression profiling by light-sheet microscopy
Quality Control Metrics: Tracking in at least 2 mice per sex
Key Factors for Metadata: Mouse line RRID#, in-house husbandry conditions, instrumentation platform, analysis software version #
Data Repositories: Primary data in-house, to be made available upon request; knowledge summary in KMC
Tracking Identifiers: DOI for weblink
Release Policy: Available immediately after QC metrics met (20% delayed until pre-print deposition in bioRxiv)
Specific examples of different quality metrics based on different classes of physical resources and reagents:
Antibody Resources: Measurable signals are not detected in negative controls lacking the expression of the target protein.
Cell-based Resources: Mycoplasma contamination testing, karyotyping and genomic testing for modifications to detect genetic drift.
Chemical Probe: Chemical Probe: Potency: In vitro potency of <100 nM; Selectivity: >30-fold selectivity vs other subfamilies; Cell activity: Significant on-target cell activity at 1 µM; Negative control. Follow probe definitions by SGC.
Chemical Resources: Quality control metrics will be adopted from the American Chemical Society, purity >95% by HPLC for distribution and synthetic chemical route.
Chemical Tool: Potency: IC50 <100 nM for dark kinase; Selectivity: S10 at 1 uM <0.05 in large kinome panel; Cell activity: IC50 <1uM by NanoBRET assay
Genetic Constructs: Addgene provides full re-sequencing of all constructs provided.
(link: https://help.addgene.org/hc/en-us/articles/206135535-What-type-of-Quality-Control-does-Addgene-perform)
Mouse Lines: Genotype testing, modification identification, pathogen screening, cryopreservation/cryorecovery and viability. Follow MMRRC quality control and reproducibility assurances.
(link: https://www.mmrrc.org/about/Reproducibility_Assurances_Handout_DS.pdf)
Peptide Resources: High-quality peptides that satisfy the guidelines by the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium ( CPTAC).