EIGC Methods and Instrumentation

The facility is CLIA certified (CLIA:11D1086150).  Our SOPs include DNA and RNA extractions from FFPE, fresh blood, frozen blood, PBMC, buffy coat, saliva, stool, tissue, cell pellet, and swabs (vaginal, rectal, buccal) samples.  We have the capacity to perform DNA and RNA extractions from other custom samples.  Read more about CLIA services.

Confirm knock-out and knock-in genome edits.

Taqman genotyping and gene expression

Applied Biosystems’ TaqMan real-time PCR assays consist of target-specific primers and one or more probes optimized for specific types of applications, including gene expression, SNP genotyping, miRNA, and copy number variation analysis.  EIGC will use our ABI 7900HT instrument to perform RT-PCR for your project.

Microarray

Microarrays are designed to capture specific genomic information from a sample, such as the presence of specific genes in a pathway, structural variants, SNVs, CNVs, methylation sites, or custom sequences. EIGC can help you to outsource microarray services.

Droplet digital PCR

Droplet Digital PCR (ddPCR) is a method for performing digital PCR that is based on water-oil emulsion droplet technology. Using BioRad’s QX200 instrumentation, a sample is fractionated into 20,000 droplets, and PCR amplification of the template molecules occurs in each individual droplet.  Fluorescent probes designed to detect specific DNA sequences are utilized to determine the presence of a DNA target of interest.  PCR-positive and PCR-negative droplets are counted to provide absolute quantification of target DNA in digital form.  Assays include absolute quantification, copy number variant analysis, rare mutation and sequence detection, gene expression, and detection of genome editing events.

Bruker/NanoString nCounter Technology

Bruker's nCounter FLEX Profiler allows analysis of tens to hundreds of targets from DNA, RNA, and protein samples.  The Bruker panels are available in pre-curated or custom panels.  EIGC will help the investigator to determine the best panels for a project and will perform the assay on the nCounter FLEX Profiler using extracted DNA, RNA, or lysate.  Read more about nCounter.

Library Sequencing

EIGC can provide library quantification services and sequencing services on our Illumina NextSeq 2000 Illumina MiSeq, or ONT Nanopore GridION instruments.  EIGC can help you to outsource sequencing projects which cannot be supported by the instrumentation on site.

Whole genome sequencing

Whole genome sequencing is a comprehensive method for evaluating the entire genome of a sample.  Each sample requires around 90 Gb of sequencing.  The EIGC will help the investigator outsource the whole genome sequencing project, finding the best platform and pricing for their needs. 

Whole exome sequencing

Whole exome sequencing is a method to evaluate the protein-coding regions of the genome, allowing one to detect coding variants in a sample.  Whole exome sequencing may be a more cost-effective approach than whole genome sequencing for some scientific questions.  Each exome requires around 4-5 Gb of sequencing. The EIGC will help the investigator outsource the whole exome sequencing project, finding the best platform and pricing for their needs.

Single cell sequencing

Single cell sequencing is a technology that barcodes the DNA from individual cells with unique barcodes, allowing independent detection of genomes from each cell.  EIGC has the 10X Genomics Chromium Controller.  Single cell assays available with the 10X Genomics Chromium Controller are Single Cell RNA-Seq, Single Cell Immune Profiling, Single Cell ATACseq, and Multiome. See RNA-Seq (Single Cell) in the Transcriptomics section below for more information.

Targeted sequencing

Targeted sequencing allows Next Generation Sequencing of specific genes of interest.  EIGC works with investigators to design primer assays using the Standard Biotools D3 Design tool, and we use the Standard Biotools Targeted Sequencing assays on the Standard Biotools X9 system to prepare libraries for sequencing.  Each LP 48.48 IFC allows NGS of up to 48 samples, using up to 4800 multiplexed assays.

Amplicon (16S rRNA)

16S rRNA sequencing determines the microbial populations present in a sample using the 16S rRNA variable regions which distinguish phylogenetic classes of prokaryotes.  The EIGC currently supports sequencing two different 16S rRNA gene regions: V4 only and V3-V4.  V4 has a higher read pass rate, but lower ability to discriminate taxa in a sample. V3-V4 is a longer fragment resulting in a lower read pass rate but generates data with greater power to classify taxa and is the recommended region for new projects.  EIGC will prepare amplicon libraries from cell, tissue, fecal, or swab samples and sequence the libraries in-house.  Read more about 16S.

Shotgun metagenomics

Shotgun metagenomics sequencing provides a platform for sensitive detection of unculturable microorganisms and those which are less abundant in culture. This method comprehensively samples all genes in a bacterial sample in order to determine the taxonomy present in each sample.  EIGC will help the investigator to outsource shotgun metagenomics services.

RNA-Seq (Bulk)

RNA-Seq determines the expression and sequence of RNA transcripts in a sample.  The EIGC can perform RNA-Seq or will help the investigator outsource the RNA-Seq project, finding the best platform and pricing for their needs.  Read more about bulk RNA-Seq.

RNA-Seq (Single Cell)

Single cell RNA-Seq determines the expression profile of individual cells within a sample.  EIGC uses the 10X Genomics Chromium X Controller to prepare single cell sequencing libraries.  Sequencing of the prepared libraries can be performed in-house or outsourced, depending on sample size and coverage needs.  Read more about single cell RNAseq.

ATAC-Seq

ATAC-Seq generates a global map of accessible chromatin on as few as 100 cells and up to 50,000 cells.  EIGC will prepare and sequence the ATAC-Seq libraries in-house.  Read more about ATAC-Seq.

ChIP-Seq and Cut&Run Library Prep

ChIP-Seq/Cut&Run provides a map of DNA sequences which interact with specific chromatin-associated proteins.  EIGC will provide library prep and sequencing services for your ChIP’ed samples.  (We do not perform the ChIP assay, but we can help you to outsource this service).

Reduced Representation Bisulfite Sequencing (RRBS)

RRBS maps CpG sites in the genome using restriction enzymes which cut at CG-containing DNA.  This service can be a cost-effective alternative to bisulfite sequencing of the whole genome.  Read more about RRBS.

Olink Reveal

The Olink Reveal platform is based on Proximity Extension Assay (PEA) technology coupled with next-generation sequencing (NGS) to measure protein biomarkers across multiple samples in a high-throughput and sensitive manner.

Spatial profiling reveals the transcriptome or proteome within an area defined on a slide.

10X Genomics Visium spatial profiling utilizes a special slide with a grid of capture areas, and the transcriptome is determined within each capture area.

EIGC can help you to outsource other spatial workflows.

We offer mutagenesis and subcloning services for your cloning needs.  Read more about custom cloning.

TissueLyser II. Performs tissue homogenization for DNA and RNA isolation.

Kingfisher Flex: A magnetic particle processor which provides automated extraction of RNA from FFPE tissue in 96-well format and DNA from FFPE tissue, fresh or frozen tissue, blood, blood products, saliva, urine, and cell cultures in 24-well or 96-well format.

Eppendorf epMotion 5075t: A liquid handling instrument which is compatible with NGS library preparation used for preparation of NGS libraries and bead cleanup.

AirClean PCR Workstation: Provides a clean air environment in order to prevent sample contamination.

Covaris E220 Adaptive Focusing Instrument: Employs ultrasonic pulses to uniformly shear nucleic acids, in a multi-sample format with walk away operation. The instrument can also be used to automate lyses of difficult samples (like mouse tail), shear proteins, and form lipid vesicles.

Agilent Fragment Analyzer (48/96 wells): A parallel capillary electrophoresis instrument designed to speed nucleic acid fragment analysis and quality control before moving onto downstream applications.

Agilent 2100 Bioanalyzer: Allows for rapid quantification of nucleic and proteomic samples, while providing information about the size distribution of the fragments.

Nanodrop One Spectrophotometer: A UV-Vis Spectrophotomter which quantifies and qualifies DNA, RNA and protein samples from microliter volumes.

Tecan Infinite M200 Pro: Quantitates nucleic acids using either PicoGreen or RiboGreen fluorescence protocols.

Qubit: A device which reads fluorescent assays in order to quantify DNA, RNA, and protein.

Applied Biosystems 7900HT: Is a real-time quantitative PCR system that combines 96- and 384-well plate compatibility with fully automated robotic loading. Key applications include gene expression quantitation and the detection of single nucleotide polymorphisms (SNPs) using the fluorogenic 5' nuclease assay.

Applied Biosystems 7900HT: Is a real-time quantitative PCR system that combines 96- and 384-well plate compatibility with fully automated robotic loading. Key applications include gene expression quantitation and the detection of single nucleotide polymorphisms (SNPs) using the fluorogenic 5' nuclease assay.

BioRad QX200 Droplet Digital PCR System: Droplet digital polymerase chain reaction was developed to provide precision quantification of nucleic acid target sequences. ddPCR measures absolute quantities of nucleic acid molecules encapsulated in discrete water-in-oil droplets by measuring the fluorescence generated by binding of gene-specific probes or EvaGreen double-stranded DNA binding dye within each droplet. ddPCR has the ability to detect gene copy number variation, detect rare sequences from tumor cells, measure gene expression levels, and to detect genome edits (HDR and NHEJ).

Standard Biotools X9: A liquid handling instrument capable to generate targeted genomic libraries for Illumina sequencing as well as to perform gene expression qPCR in a multiplex system.

Nine Thermal Cyclers: Four Applied Biosystems 9700 Peltier-driven thermal cyclers, one MJ BioRad thermal cyclers, one Eppendorf Mastercycler, three BioRad C1000 and one BioRad Tetrad with four 96-well gradient capable blocks.

Covaris E220 Adaptive Focusing Instrument: Employs ultrasonic pulses to uniformly shear nucleic acids, in a multi-sample format with walk away operation. The instrument can also be used to automate lyses of difficult samples (like mouse tail), shear proteins, and form lipid vesicles.

Standard Biotools X9: A liquid handling instrument capable to generate targeted genomic libraries for Illumina sequencing as well as to perform gene expression qPCR in a multiplex system.

10x Genomics Chromium X Controller: An automated system that allows one to encapsulate samples into hundreds to tens of thousands of uniquely addressable partitions in minutes, each containing an identifying barcode for downstream analysis. Supports a wide variety of assays when combined with Illumina sequencing that include: Single Cell Gene Expression, Single Cell Immune Profiling, Single Cell Copy Number Variant Detection, Single Cell ATACseq.

Invitrogen Countess: A digital cell counter and viability instrument.

One Illumina MiSeq instrument: A fully integrated next generation sequencing platform capable of generating between 540 Mb (~4 hours) up to 8.5 Gb (~39 hours) of raw sequence. Some applications of this platform include targeted sequencing from complex eukaryotic genomes or cancer tumors, microbial whole-genome sequencing, 16S rRNA sequencing for microbiome studies, and viral genome sequencing. Sample preparation is rapid and samples can be multiplexed with following unique indexing.

One Illumina NextSeq 2000 instrument: A fully integrated next generation sequencing platform capable of generating between 10GB to 540GB in instrument runs that range between 8 to 44 hours per experiment. Some applications of this platform include sequencing RNAseq, ATACseq or single cell libraries, targeted sequencing from complex eukaryotic genomes or cancer tumors, microbial whole-genome sequencing, sequencing of bisulfite treated DNA for assessing methylation, and sequencing other custom libraries.

Nanopore GridION: A sequencing device which provides long-read sequencing capabilities for RNA, cDNA, and DNA using the MinION flowcell.

Large-Scale Next Generation Sequencing: The EIGC has adopted an innovative business model whereby large-scale next-generation sequencing is outsourced to other academic and commercial entities, with the ultimate goal of obtaining the lowest cost, highest quality, and fastest turn-around for our customers. Academic partners include genomics core facilities at Emory Primate Center, the University of Georgia, Georgia Institute of Technology, and New York University. Commercial companies include: Discovery Life Sciences, Novogene, Omega Bioservices, Genewiz, Tempus, and Otogenetics. We have the flexibility to pursue sequencing projects with any outside provider that provides competitive pricing, rapid turn-around time, and high-quality data. In effect, the EIGC acts as a sequencing service broker, whereby we compete companies against each other to obtain the best pricing and service for Emory investigators.