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Services - Laboratory Services

GRC Lab Services, click on image to expand

Using multiple complementary high-throughput platforms, we provide a full range of genomic laboratory services. In addition to the sequencing applications listed below, we perform sample preparation and quality control assessment for each of our platforms, and also provide customized applications and methods development. Each sequencing service includes data processing, quality control, and delivery. We deliver high-quality, filtered sequence data and associated quality scores via Aspera file transfer,hard media, or NCBI deposit. Our laboratory services can be combined with our analysis services to provide comprehensive data generation and analysis for your project. Services are provided on a fee-for-service basis and each project is customized to the needs of the investigator.

For more information or to discuss your research needs, please request a consultation.

DNA/RNA Extraction

We purify DNA and RNA from a wide variety of sample types, including human, animal, and environmental origins to suit project requirements. Nucleic acids are primarily used as input template for DNA, RNA, or amplicon library preparations. We can prepare high molecular weight genomic DNA for long-insert sequence libraries as well as traditional DNA/RNA extractions. Total nucleic acids (DNA+RNA) can be extracted in high throughput (4x96 samples per day) for large scale genomics projects.

Library Preparation

We perform a full range of DNA and RNA library preparation for each of our platforms. These libraries range in size from short miRNA libraries to >40kb ultra-long insert libraries for de novo assembly. We can prepare libraries from as little as 250pg to as much as 30ug of DNA or RNA.

Genomes/Metagenomes

We sequence everything from small viruses to human genomes and large plant and animal genomes. In the absence of a finished or high-quality draft reference genome sequence, we utilize one or more of our platforms in combination to generate a high-quality de novo genome assembly. For comparative genome resequencing, we customize the platform and coverage to meet the analysis goals of the project. We can scale projects from single samples to multiplexing hundreds of samples per run.

For metagenomes/microbiomes, we use multiple platforms depending on the project. We sequence DNA isolated from an organismal or ecological sample to investigate the constituent community of organisms and functional profile present in the sample.

Exomes and Custom Capture

For many projects, identification of variants within protein coding sequences is both more effective and more efficient than whole genome sequencing. Using sequence capture technologies in combination with Illumina or PacBio sequencing, the GRC generates high-quality enriched exome sequences. These capture technologies can also be used to target customized regions of the human genome or other genomes. We have successfully used this technology to capture and sequence the genomes of multiple unculturable or difficult-to-isolate pathogens.

Transcriptomes/Metatranscriptomes (RNA-Seq)

One of the fastest growing areas of genomics, this application can be used to answer questions about gene expression and regulation and to discover novel transcripts, SNPs, and splice variants. Strand-specific RNA-Seq can identify the sense strand for each transcript. Different library construction methods can be used to target mRNA only or combinations of mRNA, miRNA, ncRNA, and other families of RNA molecules. In collaboration with faculty investigators at IGS, the GRC developed a method for simultaneous sequencing of host and pathogen transcriptomes in infected cells. The PacBio Iso-Seq method enables long-read sequencing of full-length transcripts to better identify and reconstruct isoforms. An RNA-Seq approach to a metagenomic sample can be used to generate metatranscriptomic data that describes the combined expression profile of the community.

Epigenomes

The Illumina platform enables the investigation of DNA-protein interactions and DNA methylation through the sequencing of chromatin-immunoprecipitated (ChIP) DNA and bisulfite converted DNA respectively. Resulting data can be aligned to a reference genome to generate maps of protein binding positions and methylation sites. The ATAC-Seq method can be used to identify regions of chromatin open to transcription or binding of transcription factors. The PacBio SMRT sequencing technology can be used to natively detect a wide range of modified nucleotides and motifs.

Microbiome Amplicons (16S, 18S, ITS, etc.)

Our microbiome service is flexible to address project needs but primarily makes use of the Illumina sequencing platform. We offer library preparation services tailored to desired target amplicons (16S, 18S, ITS, custom) as well as amplicon region (V1-V3, V3-V4, V4, V4-V5 etc). Sequencing is conducted on Illumina MiSeq or HiSeq 2500 using paired-end 300 bp reads. The microbiome service is coupled with bioinformatic processing to produce taxonomic assignment, absolute abundance (qPCR) and summary statistical reporting. Full-length 16S rRNA sequencing is also an option using the PacBio Sequel II instrument.

Single Cell Sequencing

Single cell sequencing applications are among the fastest growing in the field. We utilize the 10x Chromium platform to capture hundreds to tens of thousands of single cells for gene expression profiling, ATAC-Seq, immune profiling, and genome scale linked-read sequencing for de novo assembly. For applications targeting lower throughput single-cell assays, we have a customized ultra-low-input library preparation pipeline for single cells sorted into 96-well plates.

Customized Amplicons

High-throughput amplicon sequencing can be used to sequence many viral genomes in parallel, validate hundreds of variants identified in previous experiments, or sequence any combination of multiplexed amplicons. Depending on the goals and scale of the project, any of our sequencing platforms can be used for this application.

Digital Molecular Profiling

The NanoString nCounter Analysis System enables the profiling of hundreds of mRNAs, microRNAs, SNVs, CNVs, or protein on one platform with high sensitivity and precision. The nCounter’s digital counting capability provides highly reproducible data over 5 logs of dynamic range and does not require any amplification steps that might introduce bias to the results. An additional advantage of nCounter chemistry is that it is highly tolerant of difficult sample types such as FFPE and crude-cell lysates.

Customized Applications

Sequencing platforms and applications are ever-evolving. We strive to maintain cutting-edge technologies and capabilities. We offer customized sequencing assay development and will work with you to implement the latest protocols and applications to support your research.

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