Genomics and Bioinformatics Core

The Core provides high through-put sequencing services starting with experimental design, quality control of user materials, making sequencing library, generating sequencing results, and demultiplexing indexed samples providing raw sequencing data (FASTQ files) to the users. We use Illumina’s TruSeq Chemistry for library preparation and Illumina’s sequencing by synthesis technology for high through-put sequencing. Please use this link to submit your samples.

Illumina HiSeq4000 is our sequencing platform. HiSeq 4000 uses patterned flow cell and new exclusion amplification technology. Patterned flow cells contain billions of nanowells at fixed locations across both surfaces of the flow cell. The structured organization provides even spacing of sequencing clusters to deliver significant advantages over non-patterned cluster generation. The new exclusion amplification clustering method allows simultaneous seeding/landing of the DNA strand in the nanowell and amplification during cluster generation, which reduces the chance of multiple library fragments amplifying in a single cluster. This advanced flow cell design contributes to increased data output, reduced costs, and faster run times.

Services include, but are not limited to:

High-throughput next-generation sequencing using Illumina HiSeq 4000 platform, performed by PhD-trained scientist with nearly 20 years’ experience in genomics. Standard services include:

  • DNA sequencing (DNA-Seq) 
  • Transcriptome analysis (RNA-Seq) 
  • Small RNA discovery (smRNA-Seq) 
  • Gene regulation & epigenetic analysis (ChIP-Seq) 
  • Customized sequencing per user design
  • Single cell genomics with Fluidigm C1 IFCs

Pricing for HiSeq 4000 sequencing is broken into two components: library preparation and sequencing cost.  Library preparation is charged on a per sample basis and varies by type. Sequencing charges are based on the length of the sequencing run and whether it is a single direction, paired end.

The current charges for using these services are listed on the Genomics Services Price List. Recipients of Connecticut Stem Cell Research Fund awards and YSCC members will be charged a discounted rate.  We welcome external customers including foreign non-profit institutions.

Mei Zhong, PhD, Genomics Core’s Technical Director, working on the Illumina HiSeq 4000 sequencing system. It can generate 1.5TB of data in a single run.

Collaboration Projects:

In additional to standard services, Genomics Core offers collaboration with individual researchers who wish to go beyond the standard Illumina protocols to suit their research project needs. The Core has developed custom protocols for mRNA and ChIP libraries at considerably lower costs. We have performed SMART-Seq from very low total RNA input (e.g. <100 ng). The Core has also sequenced with customized adaptors and primers. To study RNA protein binding complex, we sequenced RIP-Seq and also screened a very large shRNA library using the same technology. The Core also performed CLIP-Seq and HiC/3C-Seq sequencing.

How to obtain service from YSCC Genomics Core and what you will expect of your data:

  • Sample:  We use the latest advancement of the TruSeq Chemistry from Illumina for all standard library preparation and Illumina sequencing by synthesis technology for high through-put sequencing. Please use this link to submit your samples.

  • Submission:  Users should submit 5-10 uL of undiluted sample (The Core will use 1ul for Bioanalyzer/Qubut for quality control. If concentration is too low, we may ask that you resubmit.

  • Data Output:  Sequencing data output and run metrics will be available for user to download through the link provided after sequence completion. Sequencing data is stored in a Yale central server for two months. When sequencing is completed, a link with sample information will be provided to an online website where you can click and download your data. For outside users, we will provide a different link for data download to only raw sequencing data FASTQ files; run metrics will not be included.

  • Turnaround Time:  Each HiSeq 4000 run processes 8 samples/lanes per run. A full flow cell of 8 samples/lanes can be run same day with results available in as little as 4 days. Partial submissions of less than 8 samples/lanes will be added to a project queue, where they joined with existing samples or await others before processing. Wait times for partial submissions vary depending on demand from other users.


Mei Zhong Ph.D.
Technical Director
Genomics Core of Yale Stem Cell Center
Yale University School of Medicine
10 Amistad Street Room 201F
New Haven, CT 06520

Phone: (203)737-6203


10 Amistad Street, Room 203
New Haven, CT 06520