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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.

To request Next Gen Sequencing services, follow the directions below:

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. 
 

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 (100X coverage)
24
3
n/a
16s Samples with >100,000 read coverage n/a
n/a
288
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:

  • A request must be made using the iLab Operations software

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

  • The Core will not begin processing samples until a request is made and samples are submitted correctly.
  • Submit final libraries in 1.5ml tubes, clearly labeled with sample name, the date, your name/initials
  • Provide a minimum of 15ul per final library
  • For large volume samples, provide samples in 96-well FULL SKIRT plate, with a minimum of 15ul per library. Clearly label the outside edge with user name, project name, and date. DO NOT LABEL THE SEAL. 

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 library pool will be diluted and denatured for sequencing following Illumina protocols. All fees for final library QC 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 run data is shared with the user via secure log-in FTP site, where files are available for download for 30 days. MiSeq run data is saved for six months in BaseSpace, Illumina’s cloud, and access is shared with the user. Back-ups of all HiSeq and MiSeq runs are stored for six months by the Core on a separate hard drive.

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 70 percent of the maximum number of possible reads as listed by Illumina based on instrument type and reagents used only if the Core completes all quality control (QC) on submitted total RNA and/or DNA and performs the library prep, final library prep QC and pooling. 

If at any time the Core has given an opinion at any point in the process that a particular sample and/or run should not be sequenced due to failed QC and the user overrides the advice, the Core can not guarantee the run. The responsibility of the run will be on the user.