Services

Genome Editing Services

Project consultation / experimental design

All projects begin with a discussion to determine the most effective strategy for achieving the investigator’s goals. Typically, the most productive conversations start with the investigator simply telling us the change needs to be made to the genome. From there, we work together to determine for each investigator’s project, what are the most important parameters (minimizing off target effects, efficiency of mutagenesis, cost, etc.). Once an optimal experimental plan is decided, we work together with the investigator to complete the genome editing project. Go to the CONTACT page to initiate a project by filling out the Project Initiation form.

 

Generate customized DNA reagents

We make the linear DNAs and/or plasmids needed for an efficient genome editing project. The investigator then takes these reagents and is responsible for introducing them into the target of choice (cell line or organism).

 

Synthesize RNA reagents for injection

For some projects, such as mutation of genes in mice, injection of RNA works better than DNA. We will make the RNA in a quality-controlled, RNAse-free setting and test the quality of each preparation.

 

Provide reagents for screening

One of the most confusing parts of a project can be ensuring that a cell (or organism) actually has the desired genome edit, and only the desired change. In addition to consultation, we will provide the DNA reagents and guidance on performing a screen to select only the right cells.

 

Make an edited cell line for you

Tell us exactly what change you want to make to the genome of your favorite cell line, and we will make it for you.

 

Make an edited mouse for you

We will make the reagents and have them injected. Making small targeted deletions and indel mutations follow the “Knockout mouse” fee structure, below.

 

Prepare mouse ES cells for blastocyst injection

If you have a clone that you want injected to make a chimera, we will thaw the cells and prepare them for injection.

Please note, Investigators from the Northwestern University and the University of Chicago are provided internal rates as all UIC users. All other users can access services but, at either external academic or external non-academic rate.

Genomics Services

  • Affymetrix 3’IVT Amplification and Labeling
  • Affymetrix Array – Gene 2.0 ST
  • Affymetrix Array – HTA 2.0
  • Affymetrix Array – miRNA 4.0
  • Affymetrix Array – PrimeView
  • Affymetrix Array: Promoter 1.0R
  • Affymetrix FFPE Amplification and 3′ IVT Labeling
  • Affymetrix FFPE Amplification and WT Labeling
  • Affymetrix FlashTag Labeling
  • Affymetrix GeneChip Hybridization, Wash, Stain, and Scan
  • Affymetrix Tiling Array: Fragmentation and Labeling
  • Affymetrix WT Amplification and Labeling
  • Automated Pipetting: Eppendorf EpMotion
  • DNA barcoding
  • Expression Analysis Part 1
  • Expression Analysis Part 2: Gene Network and Pathway Analysis (MetaCore)
  • Expression Analysis: MetaCore Training
  • Expression Analysis: MetaCore Unassisted Use
  • Fluidigm – BioMark 192.24 Gene Expression
  • Fluidigm – BioMark 96.96 Dynamic Array Chip for Gene Expression
  • Fluidigm – BioMark Flex Six IFC
  • Fluidigm – C1 Single-Cell Capture
  • Fluidigm – Cell QC
  • Genome-Wide Cytogenetic Analysis: Affymetrix CytoScan or OncoScan Arrays
  • Genome-Wide Gene Regulation Analysis: Affymetrix Tiling Array
  • Genome-Wide Genotyping: Affymetrix Array
  • Genome-Wide small non-coding RNA Profiling: Affymetrix miRNA Array
  • Genome-Wide Transcriptional Profiling: 3’ Affymetrix Array
  • Genome-Wide Transcriptional Profiling: RNA-seq
  • Genome-Wide Transcriptional Profiling: Whole-Transcript Affymetrix Array
  • MeDIP sequencing
  • Targeted Genotyping: Sequenom Cancer Mutation Panel
  • Targeted Genotyping: Sequenom Customized SNP Panel
  • Targeted Methylation Analysis: Sequenom
  • Targeted Methylation Profiling by Sequencing
  • Targeted Transcriptional Profiling: Real-Time PCR Based Assays

Sequencing Services

Daily Capillary Electrophoresis Sequencing Services

  • Same Day Sequencing Service
  • Standard Sequencing Service
  • Standard Sequencing Service for Ready-To-Load Plates (24-47RXNs)
  • Standard Sequencing Service for Ready-To-Load plates (48-96RXNs)
  • Template Preparation from Culture for Sanger Sequencing (mini-prep)

To request this service, please click here.

 

Nucleic Acid Extraction, Quantification, and Quality Analysis Services

The SQC has instrumentation and highly trained staff for a wide range of extraction protocols. Instrumentation includes two Promega Maxwells, Qiagen QIACube, and a Qiagen EZ1 extraction robot. Most sample types can be extracted at the SQC, including but not limite to, feces, tissues, cell cultures, FFPE (DNA and RNA), soil, filters, etc. The facility maintains BSL2 laboratories for extraction of BSL2 pathogens and samples with pathogenic potential. Nucleic acids can be assessed for quality and quantity using agarose gel electrophoresis, automated gel electrophoresis using our Agilent TapeStation devices, Nanodrop quantification, Qubit quantification, and Picogreen quantification using a 96-well plate reader.

To request these services, please click here.

 

Quantitative Analyses of Nucleic Acids

 

The DNAS facility provides quantitative PCR instruments for customer use (ABI 7500 and ViiA7 instruments) through a registration system in our lab management software, iLABs. In addition, DNAS staff are highly experienced in performing reverse transcription, pre-amplification, assay selection, plate loading, qPCR operation, and data analysis. On a fee-for-service basis, our staff can conduct qPCR projects according to investigator requests. In addition to standard qPCR, the facility also maintains a digital PCR device (Life Technologies QuantStudio3D) for absolute quantification of targets and for measuring allele frequency (for example). Finally, our facility performs extraction-independent RNA sequencing of human cells and tissue (fresh/frozen/FFPE) using the BioSpyder TempO-Seq protocol.

To request this service, please click here.

 

Fragment Analysis Services

 

Fragment analyses are performed on our ABI 3730xl DNA Analyzer in a 96-well format. Samples can be provided in water or formamide. We provide internal standards (Only LIZ1200 and LIZ600) for analyses. Please contact our core for details regarding sample submission.

We also perform cell line authentication service using short tandem repeat analysis.

For microbial ecologists, we also provide automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (TRFLP) analyses.

To request this service, please click here.

 

Amplicon-Based NGS Sequencing for Microbiome Studies

 

High-throughput next-generation sequencing of short (<520 bp) amplicons is an area of expertise for the DNAS facility. Samples can be processed from genomic DNA or from PCR products (when produced according to facility instructions). Briefly, a two-stage PCR amplification protocol is used to generate amplicons containing Illumina sequencing adapters, a sample-specific barcode sequence, and the amplification target. These amplicons are purified and pooled together and sequenced using paired-end sequencing on an Illumina MiSeq instrument. In general, 20,000-50,000 sequences per sample are generated. A full bioinformatics pipeline for microbial 16S ribosomal RNA gene annotation and analysis has been developed with UIC’s Center for Research Informatics (CRI). See our microbiome pamphlet for more details.

To request this service, please click here.

Visit our Research Informatics Core to learn more about in-depth data analysis services.

 

Library preparation and sequencing of DNA and RNA templates using NGS platforms

 

The DNAS facility operates an Illumina NextSeq500 sequencer for high-data sequencing demands, including: genome sequencing/re-sequencing, RNA-seq, ChIP-seq, hybridization target-capture sequencing, shotgun metagenome and metatranscriptome sequencing, and other applications. Library preparation protocols used include DNA-based library preparation protocols including KAPA Hyper, Illumina NeoPrep, Illumina Nextera and Nextera XT, and others. Library preparation protocols for RNA-sequencing are primarily conducted by the Core Genomics facility, and include: Lexogen 3’-mRNA-seq, Lexogen SENSE, Illumina TruSeq, and BioSpyder TempO-Seq. Ribosomal RNA depletion using RiboZero or RiboMinus can be performed as well. Contact directors of DNAS, CG and CRI facilities for discussions on choosing the appropriate sequencing strategy and appropriate sequencing depth and experimental design (particularly number of replicates). Data are generally delivered using Illumina’s BaseSpace cloud storage and analysis environment. The NextSeq500 instrument can generate from 20-150 Gb of sequence data in 75-150 base reads, in single-end or paired-end read mode. For de novo bacterial genome sequencing, DNAS has partnered with external facilities to perform PacBio sequencing, and we have acquired an Oxford Nanopore sequencing device.

To request this service, please click here.

Visit our Research Informatics Core to learn more about in-depth data analysis services.

Please note, Investigators from the Northwestern University and the University of Chicago are provided internal rates as all UIC users. All other users can access services but, at either external academic or external non-academic rate.