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Genomics Core

Next Generation Sequencing

Next Generation Sequencing

Next Generation Sequencing (NGS) Services

A Next Generation Sequencing machine on a table.For Next Generation Sequencing (NGS) Services, the CWRU Genomics Core operates two Illumina HiSeq 2500 DNA Sequencers and one MiSeq desktop sequencer. One HiSeq is designated for v4 High Output flowcells and the other is used for running v2 Rapid Run flowcells. The MiSeq has the capability of running all v2 and v3 flowcells available. Collectively, the Core is able to handle a wide range of applications and different sized projects at the same time.

  • RNA-seq
  • miRNA-seq 
  • DNA-seq
  • ChIP-seq
  • Whole Genome Sequencing (WGS)
  • Whole Exome Sequencing (WES)
  • Amplicon Sequencing including CRISPR
  • 16S Metagenomics

To set up a consultation for a project, or if you have any questions, please contact the Genomics Core Director, Dr. Alexander Miron, at 216.368.2791 or at alexander.miron@case.edu. For project quotes, please contact Simone Edelheit, Core Manager, at 216.368.1887 or at sxw94@case.edu.

 

NGS Run Options & Outputs

View the table below to determine which platform is best suited for your project:

 HiSeq 2500 HIGH OUTPUTHiSeq 2500 v2 RAPID RUNMiSeq V3 FLOWCELL
Number of Lanes per Flowcell
8
2
1
Reads per Lane
250 million
150 million
25 million
Reads per Flowcell
2 billion
300 million
25 million
Maximum Read Length
2x125bp
2x250bp
2x300bp
RNA-seq/ChIP-seq samples per flowcell
40
6
n/a
WES samples/flowcell (TS Rapid kit)
40
6
n/a
16s Samples with >100,000 read coverage n/a
n/a
96
CRISPR-cas gene editing samples
n/a n/a 192
 
     
 
**ALL HO runs require a MiSeq Library QC run**     

For a list of all runs types available and pricing, please see Pricing.

 

Sample Submission

An individual holding three types of Illumina flowcells that can be run at the Genomics Core: the HiSeq 2500 High Output, the HiSeq 2500 Rapid Run, and the MiSeq v3 flowcells.The Genomics Core accepts samples in two different stages:

  1. gDNA or total RNA – library prep completed by the Core. See service >
  2. Final Library – library prep completed by the user

Final Library Requirements:

  • Provide a minimum of 15ul of each Final Library or Final Library Pool. 
  • Submit all samples in a 1.5ml tube, clearly labeled ON TOP OF TUBE with sample name and user name/initials (sample name on request form and on tube should match). Label the SIDE OF THE TUBE with the date.
  • Large volume projects may be submitted in FULL SKIRT 96-well plates, with at least one SIDE WALL clearly labeled with project name, plate number, user name, and date. Sample names and well location will be submitted through iLab. 
  • To begin a request for services, please follow the iLab instructions:

    The Genomics Core is now transitioning all service requests over to iLab Operations Software, a part of Agilent Technologies’ CrossLab platform. This is an online system to streamline the process of ordering and billing for core service requests. 

    In order to gain access to your funds you will need to begin by logging into iLab at the following web address:

    https://cwru.corefacilities.org

    Once an account is created, the Genomics Core ordering site can be found here:

    https://cwru.corefacilities.org/service_center/show_external/4142?name=genomics-core-facility

    Simply click on Request Services tab to begin. 
     
  • The Core will not begin processing samples until a request is made and samples are submitted correctly.

Whether prepared by the user or the Core, all final libraries will undergo quality control (QC) prior to running on the Illumina sequencers. The Core will run Qubit for concentration (ng/ul) and Agilent Bioanalyzer High Sensitivity DNA chip for library quality and average fragment size (bp). If samples pass QC, they will be pooled equally and according to adapter-indexes used. The pool will be quantified using the KAPA Biosystems Library Quantification kit. The final library pool will be diluted and denatured for sequencing following Illumina protocols. All fees for Final Library QC, pooling, and qPCR are separate and not included in the cost of a run. Additional charges to each project vary depending on which QC services are completed. 

Run Analysis and Data Collection

Upon completion of a run, the data is automatically sent through a series of custom pipelines. FASTQ files are generated for all samples within a run and provided to the user in Illumina 1.8x format. We perform quality control (QC) of the run using software provided by Illumina as well as FastQC to confirm that high quality data is provided.

Data is released to the user once it has passed our quality checks. All HiSeq and MiSeq run data are shared with the user via secure log-in FTP site, where files are available for download for 30 days. MiSeq run data can be shared via BaseSpace, Illumina’s cloud. Back-ups of all HiSeq and MiSeq runs are stored for six months by the Core. It is the responsibility of the user to keep a back-up of all data provided by the Core. 

NGS Run Guarantees

Each Illumina NGS platform delivers a maximum output dependent upon the type of flowcell and reagents used. In practice, this output can also be affected by the DNA source and the type of library created. It is our goal to have each run collect the highest quality and quantity of data possible for the set of samples being run.

The Genomics Core will guarantee a minimum of 80% of the maximum number of possible reads as listed by Illumina based on instrument type and reagents used if the Core completes all quality control (QC) on submitted total RNA and/or DNA and performs the library prep, final library QC, pooling and qPCR. All libraries used must pass QC in order for the run to be guaranteed. 
 
The Genomics Core will guarantee a minimum of 70% of the maximum number of possible reads as listed by Illumina based on instrument type and reagents used if the user submits final library preps that use all standard Illumina reagents (ie: primers) and the Core completes final library QC, pooling and qPCR. All libraries used must pass QC in order for the run to be guaranteed.  
 
It is our goal to have each run collect the highest quality and quantity of data possible for the set of samples being run, however at times there are limitations. The Core cannot guarantee a minimum data output in the following cases: when a run is performed using QC data provided by the user, if any custom sequencing/indexing primers are used in replacement of Illumina provided reagents, or a run that includes experimental libraries that have not been previously tested at our core or by Illumina.