Document text
Principal Investigator: Ioannis Vlachos
Organization: BETH ISRAEL DEACONESS MEDICAL CENTER
Fiscal Year: 2024
Award: $303,065
Funding agency: National Institute of Allergy and Infectious Diseases
SUMMARY
The proposed multi-disciplinary Program Project Grant (PPG) will utilize interdisciplinary expertise, key
established resources, cutting-edge technologies, and extensive in vivo and human studies to bypass
substantial roadblocks in our understanding, management, and treatment of lupus nephritis (LN). Core C will
leverage already established extensive resources, specialized personnel, infrastructure, and expertise to
address effectively and efficiently sample processing, data generation, ingestion, and integration, major
bottlenecks in spatial/single cell profiling. Core C will prioritize data provenance and best practices,
ascertaining that all activities adhere to the FAIR principles across the data life cycle. Core C will ensure
streamlined data generation, acquisition, quality control, management, and provenance across the PPG,
achieved through 3 distinct aims: the generation of production-grade highly automated single cell and spatial
tissue profiling data (Aim 1), the establishment of streamlined data processing, quality control, management,
and provenance (Aim 2); and the promotion of best practice, scalable, multi-modal data processing, analysis,
and integration (Aim 3).
The Core will work closely with the personnel of the Administrative Core, the Cores, and the Projects for
efficient and timely data delivery. The rich metadata captured across all activities, along with versions, code,
and extensive provenance activities, will ascertain that all datapoints adhere to the FAIR principles. By
centralizing high throughput assay performance, bioinformatics, and biostatistics the Core enables uniform
best practice analyses across all activities, effective data integration, seamless reuse, interoperability, and
cost-effectiveness.
All pipelines and protocols will be shared to facilitate the community to recreate findings and build upon this
effort. Wherever possible, pipelines will be provided as complete workflows or containers for easy deployment
in diverse environments. We will build upon our experience of implementing production grade assays and
impactful bioinformatics/data resources that are trusted by researchers worldwide.
Terms: <Address><Administrative Personnel><Assay><Benchmarking><Best Practice Analysis><Bio-Informatics><Bioassay><Bioinformatics><Biological Assay><Biostatistics Core><Body Tissues><Bypass><Cell Body><Cells><Cellular Assay><Code><Coding System><Communities><Data><Data Provenance><Deposit><Deposition><Disease><Disease Progression><Disorder><Dysfunction><Ensure><Environment><Evolution><FAIR data><FAIR guiding principles><FAIR principles><Findable, Accessible, Interoperable and Re-usable><Findable, Accessible, Interoperable, and Reusable><Functional disorder><Generations><High Endothelial Venule><High Throughput Assay><Human><Human Resources><Image><Immune><Immunes><Inflammatory><Infrastructure><Ingestion><Investigators><Kidney><Kidney Urinary System><Life Cycle><Life Cycle Stages><Lupus Glomerulonephritis><Lupus Nephritis><Manpower><Metadata><Modern Man><Molecular><Outcome><P01 Mechanism><P01 Program><Pathogenesis><Patient Monitoring><Patients><Performance><Physiopathology><Population><Procedures><Process><Production><Program Project Grant><Program Research Project Grants><Protocol><Protocols documentation><Quality Control><Research Personnel><Research Program Projects><Research Resources><Researchers><Resolution><Resources><Role><Sampling><Sampling Studies><Services><Single-Nucleus Sequencing><Technology><Testing><Therapeutic Uses><Tissues><Trust><Urine><Work><arm><benchmark><cell assay><cohort><computerized data processing><cost effectiveness><data acquisition><data acquisitions><data integration><data pipeline><data processing><data resource><experience><high throughput screening><imaging><in vivo><ingest><insight><interoperability><life course><lipid based nanoparticle><lipid nanoparticle><meta data><multi-modal data><multi-modal datasets><multidisciplinary><multimodal data><multimodal datasets><novel><pathophysiology><patient stratification><peripheral blood><personnel><programs><prospective><renal><resolutions><sNuc-Seq><single nucleus RNA-sequencing><single nucleus seq><single-nucleus RNA-seq><snRNA sequencing><snRNA-seq><social role><stratified patient><targeted drug therapy><targeted drug treatments><targeted therapeutic><targeted therapeutic agents><targeted therapy><targeted treatment>