Integrated Multi-Omics Facility

Enabling end-to-end studies of complex biological systems

The Integrated Multi-Omics Facility (IMOF) supports genome-scale and cell-resolved molecular profiling across genomics, epigenetics, transcriptomics, single-cell and spatial omics, and microbial sequencing. IMOF also offers comprehensive bioinformatics and computational analysis capabilities, including data processing, quality control, multi-omic integration, and advanced analytics.

Genomics

Genome-scale characterization at LLNL uses high-throughput sequencing and array-based technologies to detect genetic variants, study genome structure, and perform whole genome analysis.

LLNL’s capabilities:

• Human, microbial, plant, and animal whole genome sequencing (WGS)
• Whole exome sequencing (WES) and custom exome panels
• Single nucleotide polymorphism (SNP) profiling
• Microarray-based genomics, including the Lawrence Livermore Microbial Detection Array (LLMDA)

Transcriptomics

Researchers use high-throughput RNA sequencing to measure gene expression across tissues, conditions, and time points.

LLNL’s capabilities:

• Bulk RNA sequencing (RNA-seq)
• Total RNA/microRNA profiling
• Strand-specific expression profiling

Single-cell omics

Single cell and single nucleus omics provide cell type resolved views of complex tissues, immune responses, and heterogeneous systems.

LLNL’s capabilities:

• Single cell RNA sequencing (scRNA-seq)
• Single nucleus RNA sequencing (snRNA-seq)
• Single cell immune profiling, including V(D)J sequencing of T cell receptors (TCRs) and B cell receptors (BCRs)
• High throughput single cell workflows (barcoded and multiplexed)
• Single cell ATAC sequencing (scATAC-seq)
• Custom pathogen probe incorporation for infectious disease studies

Microbial sequencing

Microbial sequencing at LLNL supports comprehensive characterization of microbial communities, pathogens, and their functional activity. These approaches help resolve community composition, track temporal dynamics, and reveal molecular mechanisms that influence ecosystem and host outcomes.

LLNL’s capabilities:

• Metagenomic and meta-transcriptomic profiling of complex microbial communities  
• Rare variant analysis for sensitive detection of low frequency organisms or mutations
• Targeted sequencing for focused taxonomic and functional assays, including:
  • 16S and 18S rRNA gene sequencing
  • SARS-CoV-2
  • Viral enrichment (e.g., Twist panels)
  • Antimicrobial resistance (AMR) gene panel

Sequencing platforms and applications

IMOF uses leading DNA and RNA sequencing technologies and commercial platforms, including short-read Illumina instruments, long-read Oxford Nanopore and PacBio systems, and ABI capillary sequencers for Sanger sequencing. These technologies support integrated multi-omic studies of host-pathogen interactions and complex biological systems, with applications ranging from rapid diagnostics and pathogen surveillance to host immune profiling, microbial and metagenomic analysis, de novo genome assembly, and structural variant detection.