Research Services

Sequencing Services

  • 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, we generate 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)
    (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, we 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.)
    (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.

Analysis & Computational Services

  • Assembly & Annotation
    De novo assembly: Using a range of sequence assembly tools tuned to the appropriate genome size and characteristics, we produce an optimized assembly and deliver contigs, scaffolds, and metrics in a variety of standard formats.

    Genome Annotation: We provide annotation of both prokaryotic and eukaryotic genome sequences. This includes gene finding, searches of predicted proteins against various sequence-based resources (e.g. UniRef100 and Pfam), and automated annotation of proteins based on an evidence hierarchy. Visualization tools such as Manatee and WebApollo can be employed on the output.
  • Comparative Genomics
    Comparative Assembly: Given a reference sequence, data is aligned and assembled against the reference. Resulting contigs, scaffolds, and variant records are delivered.

    Prokaryotic Comparative Genomics: We have two available pipelines for comparing prokaryotic genomes. The protein cluster-based pipeline uses Jaccard filtered bi-directional best blast matches to produce ortholog clusters (Crabtree, et. al., PMID:18314579). It has been successfully used for the comparison of 100 (or more) genomes at one time. The DNA alignment-based pipeline employs the Mugsy whole genome alignment algorithm (Angiuoli, et. al., PMID:21148543). Mugsy is a reference-independent tool that builds protein ortholog groups based on whole genome multiple alignments and synteny thus helping to differentiate between paralogs and orthologs. This method is optimized for comparing closely related organisms. For both pipelines, the web-based visualization tool Sybil is used to search and view ortholog clusters, genomic context, synteny, and more.
  • Variant Analysis
    Using analysis pipelines developed specifically for variant detection, sequence data is aligned to available reference sequences. SNPs, indels (insertions and deletions), and structural variants are detected, quality-filtered, and annotated (coding, non-coding, synonymous, non-synonymous, etc.). In order to identify novel or rare variants, the variants are compared to an in-house database of known variants that includes the latest dbSNP and 1000Genomes data as well as other known variants from multiple organisms and publicly available data sets. Data visualization tools are available to browse the results. Comparative analysis of variants calls is also available.
  • Transcriptome Analysis
    Transcriptome (RNA-Seq) data can be analyzed to determine gene or isoform level expression profiles, sequence variation, and differential expression between multiple conditions and/or timepoints. Included in this pipeline is the alignment of reads to a reference genome, expression analysis, differential expression analysis, isoform analysis, and differential isoform analysis. We are also able to do de novo transcriptome assembly. Results are output as spreadsheets containing statistics, differentially expressed genes, isoforms and differentially expressed isoforms as well as pdf plots and figures such as heat maps and principle component analyses. Visualization tools such as the Integrative Genome Browser (IGV) can be used.
  • Epigenome Analysis
    We analyze ChIP-Seq, BS-Seq, ATAC-Seq, PacBio base modification, and other types of epigenomic data. Data from ChIP-Seq experiments are aligned to a reference genome and analyzed for peak enrichment to identify DNA-protein binding sites. Differential peak analysis between experiments can be used to identify binding sites specific to certain conditions or proteins. For BS-Seq or other methylation-based experiments, DNA methylation patterns are detected by aligning sequence data derived from bisulfite-treated DNA to both a reference genome and a version of the reference genome that has been in silico bisulfite converted. This dual alignment analysis enables more accurate identification of methylated sites and their boundaries. PacBio’s unique SMRT Sequencing method enables direct detection of methylation and other DNA modifications by measuring kinetic variation during nucleotide incorporation by the polymerase. Detailed base modification motif reports are generated.
  • Microbiome Profiling
    We process amplicon sequence data from 16S, 18S, ITS, and custom amplicon projects using an in-house informatics workflow that makes use of QIIME and dada2 components. This is offered primarily as a package in combination with our microbiome library and sequencing services but can also be performed on pre-existing data sets. Included in the analysis pipeline are the production of QC reports, taxonomic assignments, and assorted analysis (heatmaps, diversity measures) according to the project needs. Analysis and QC of sequence level control samples (Extraction & PCR positive/negative) is also included where applicable. Sequence data is pre-formatted for simple upload to NCBI Short Read Archive. Additional statistical analysis is offered to accommodate needs for advanced analysis relating to modeling and in-depth analysis. We offer analysis on data generated using Illumina and PacBio platforms.
  • Microarray Analysis
    We can carry out microarray analysis for samples from multiple platforms (Affymetrix Array, Affymetrix ST Array, NanoString) to study protein-coding as well as non-coding (miRNA, lncRNA, regulatory) gene expression profiles. Differentially expressed genes are identified and reported in spreadsheets, heat maps, and other outputs.
  • Pathway & Network Analysis
    Given a set of variant positions, genes, or other loci associated with a particular phenotype, we use software packages, including Ingenuity Pathway Analysis (IPA), developed specifically to analyze gene pathways and networks to find associations with functional profiles, tissue or disease specific biomarkers, and other genes in the same pathways and networks. We also use open-source network and visualization tools DAVID, Cytoscape, and Reactome to complement network/pathway analysis to increase the accuracy and sensitivity of network/biomarker identification.
  • Cloud Based Pipelines
    We are actively porting our analysis pipelines to operate in a cloud environment. Currently we have tools in the cloud to analyze whole metagenome sequence data and to perform prokaryotic genome annotation. Soon, our transcriptome analysis tools will also be cloud-enabled
  • Customized Analysis
    Our computational infrastructure and expertise enable cutting-edge custom analysis for a broad range of omics applications. We will customize an analysis plan for each project in close consultation with each investigator. Please request a consultation to discuss custom analysis projects.