Genomics & Bioinformatics Grants and Publications

Genomics & Bioinformatics Shared Resource Grant Descriptions

Short Grant Description

The Genomics & Bioinformatics shared resource has state-of-the art instrumentation and experienced staff who provide microarray, CE sequencing, next-generation sequencing, and gene modulation services. Technologies include: ABI/Life Technologies (CE sequencing and qPCR); Illumina NovaSeq 6000, Illumina NextSeq 2000, Illumina MiSeq, and Pacific Biosciences Sequel IIe (long read sequencing); 10x Genomics Chromium Controller (single-cell library prep technology); NanoString nCounter and GeoMx DSP technologies; various shRNA and siRNA libraries from Open Biosystems, Qiagen, and Invitrogen (RNAi); and drug and compound libraries from MicroSource and ChemDiv (high-throughput screening). The resource also has sophisticated data management and analysis resources, including four dedicated bioinformaticians with the expertise to assist in data processing and analysis.

Long Grant Description 

Genomics 

The genomics team, part of the Genomics & Bioinformatics shared resource, has state-of-the art instrumentation and experienced staff who provide microarray, CE sequencing, next-generation sequencing, and high-throughput screening services. Technologies include:  ABI/Life Technologies (CE sequencing and qPCR); Illumina NovaSeq 6000, Illumina NextSeq 2000, Illumina MiSeq, and Pacific Biosciences Sequel IIe (long-read sequencing); 10x Genomics Chromium Controller (single-cell library prep technology); NanoString technologies; various shRNA and siRNA libraries from Open Biosystems, Qiagen, and Invitrogen (RNAi); and drug and compound libraries from MicroSource and ChemDiv (high-throughput screening). Partnered with genomics, the bioinformatics team has sophisticated data management and analysis capabilities, including three dedicated staff members with the expertise to assist in data processing and analysis.

Sequencing: The genomics team offers both capillary-based and next-generation sequencing services. Lab staff process sequencing reactions using a dedicated Applied Biosystems 3730xl DNA Analyzer. A second 3730xl DNA Analyzer is reserved for fragment analysis applications. Services for capillary sequencing include two sample submission options, researcher-provided DNA template or ready-to-sequence cocktail. Staff provides pre- and post-data generation consultation, performs sample preparation and processing, performs data QC, assists investigators with troubleshooting, and maintains instrumentation.

Services for next-generation sequencing include RNA-seq, CUT&RUN, ChIP-seq, whole exome sequencing, targeted resequencing, pooled CRISPR screens, and numerous unique methodologies to support researchers’ needs. In addition, the lab provides and routinely employs the full suite of 10x Genomics single-cell applications, including gene expression; VDJ sequencing, TotalSeq feature barcoding and cell hashing technologies from BioLegend; combined "Multiome" profiling of gene expression and open chromatin from the same cells; and Visium spatial transcriptomics. Staff provides extensive pre- and post-sequencing consultation, sample QC, library construction and QC, sequencing, data QC, assistance to investigators with troubleshooting, and equipment maintenance. Next-generation sequencing technologies include an Illumina NovaSeq 6000, two Illumina NextSeq 2000s, two Illumina MiSeq systems and a PacBio Sequel IIe. Additional equipment includes a PerkinElmer Sciclone NGSx Workstation, two 10x Genomics Chromium Controllers, a Nanostring GeoMx DSP, a Covaris LE220, Sage Science BluePippin Prep gel system, two Agilent 4200 TapeStations, a Caliper DropSense 96 spectrometer, an Invitrogen Qubit 2.0 fluorometer, and an ABI StepOne Real-Time PCR System.

Spatial Transcriptomics: The Genomics core offers the Nanostring GeoMx Digital Spatial Profiler (DSP) for quantitative analysis of mRNA and protein in spatially defined regions of FFPE or frozen whole tissue sections.  The GeoMx DSP combines immunofluorescence and digital barcoding of mRNA and protein, using either the nCounter system or our Illumina sequencers to quantify expression levels.  The core also fully supports the Visium Spatial Trancriptomics workflows, both fresh-frozen and FFPE.

qPCR: The resource also houses four user-operated ABI QuantStudio 5 Real-Time PCR Systems, two each in a 96- and 384-well configuration. Access occurs through a centralized reservation calendar via a web-based interface.

Gene Modulation Services: The Genomics & Bioinformatics shared resource offers gene modulation services, providing libraries, robotic automation, and skilled support staff for microtiter plate-based RNAi or small molecule screens to meet the center’s varied functional genomics and drug discovery needs.

RNAi reagents consist of GIPZ lentiviral shRNA collections that include genome-wide human (155,695 clones) and mouse (57,600 clones) obtained from Thermo Scientific (formerly Open Biosystems). Clones are available to researchers through an online, searchable shRNA Storefront as either individual clones or as plasmid pools. The siRNA reagents are comprised of the Qiagen Human Transcription Factor siRNA Library (2254 genes, 4 triggers per gene), Qiagen Human Druggable Genome siRNA Library (6961, 4 triggers per gene), Ambion Silencer Select Human Kinase siRNA library (710 genes, 3 triggers per gene), a custom Qiagen Mouse Transcription Factor siRNA Library (1675, 4 triggers per gene), and Qiagen Mouse Druggable Genome siRNA Library (8353, 4 triggers per gene). Small-compound screening libraries consist of the MicroSource Spectrum Drug Library (2000 compounds) and the ChemDiv Targeted Diversity Drug Library (50,000 compounds).

In addition, the core provides consultation and custom designs for those interested in employing CRISPR-Cas9 technology into their research.

Instrumentation used to support these efforts include: a dual arm Beckman Coulter Biomek i7 with 96 and 384-channel pipettors, plus deck mounted thermocycler, dual electronic heater/chiller units, orbital shaker, and barcode reader; BioTek ELx405 plate washer with a 50 plate stacker; BioTek MicroFlo Select dispensing system with a 50 plate stacker; two Napco 8000DH C02 incubators; Motic AE21 inverted microscope; Molecular Devices SpectraMax Plus absorbance microplate reader; and Perkin Elmer EnVision Multi-label microplate reader with Enhanced Luminescence and Turbo Alpha upgrades, barcode reader, and 50 plate stacker.

Bioinformatics

The bioinformatics team of the Genomics & Bioinformatics shared resource includes four bioinformatics specialists and the resource director, who provide a wide variety of experimental design, analysis, and programming support for the genomics lab and their end users.

Most service requests to the genomics lab occur through various technology-themed modules of HutchBASE, a web-based LIMS that was developed, tested, and implemented by the resource’s staff. HutchBASE initially extended the BASE v2.6 (BioArray Software Environment, Lund University, Sweden) microarray database framework. This customized LIMS has been designed to meet the administrative, technical, and scientific needs of the Genomics & Bioinformatics shared resource and its end users. In addition to facilitating service requests, HutchBASE captures sample annotation and QC, provides sample-tracking features, manages workflows, automatically triggers data analysis pipeline protocols, produces data QC reports, affords data management capabilities, and initiates service billing reports. The database also offers the end-user electronic lab notebook capabilities for their genomics projects, through the user-defined addition of project and sample annotation fields.

A main objective for the bioinformatics staff is to support the data analysis needs of the genomics lab’s end users, with particular focus on massively parallel next-generation and third-generation sequencing. Support encompasses a wide variety of assays one might perform on a given platform including bulk and single-cell RNA-Seq, single-cell immune receptor sequencing, CUT&RUN, CUT&TAG, ATAC-seq, ChIP-seq, whole-exome variant calling, CNV analysis, pooled CRISPR-Cas9 screens. The bioinformatics staff also provide analysis support for data generated in the high-throughput siRNA and small molecule screening facility. The level of support for a given project can vary greatly and may include providing programming advice, assistance with troubleshooting R or Python code, support and guidance using commercial and academic analysis tools, and implementation of a full range of data analysis strategies that encompass in-depth data QC, various statistical analyses, and generation of summary reports and figures. Interpretation of results can be augmented by gene ontology enrichment and pathway enrichment analyses using any number of approaches (e.g., Gene Set Enrichment Analysis, Enrichr, DAVID v6.8).