Genomics and Bioinformatics Core

The Genomics and Bioinformatics Core at Yale Stem Cell Center, funded by the State of Connecticut and Yale University, supports stem cell research for research groups at Yale and in the State in gene expression experiments, transcription mapping analyses, and proteomic assays. We use the latest advancement of the TruSeq Chemistry from Illumina for both library preparation and sequencing. Please use this link to submit your samples.

One of the five core facilities of the Yale Stem Cell Center funded by the State of Connecticut and Yale University. The mission of the Genomics Core is to offer a high level of expertise in next generation sequencing technology to support stem cell research at Yale and across the State of Connecticut. The Genomics Core is a hub for collaborations and a training site for stem cell researchers who wish to extend their research using genomic approaches.

Service:

We provide services for high-throughput next-generation sequencing using illumina HiSeq 2000 platform. Standard service including:

DNA sequencing (DNA-Seq) Transcriptome analysis (RNA-Seq) Small RNA discovery (smRNA-Seq) Gene regulation & epigenetic analysis (ChIP-Seq) Multiplex sequencing (multiple samples in one lane)

Pricing for HiSeq 2000 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 or multiplex.

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.

Collaboration Projects:

In additional to the standard services, the 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 YSCC custom protocols for mRNA and ChIP libraries at considerably lower costs. The Core has also sequenced with customized adaptor & primer (ChIP-Seq) to study RNA protein binding complex. We also screened a very large shRNA library using the same technology. We have performed mRNA-Seq with a very low total RNA input (e.g. 100 ng) as well as directional transcriptome 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 both library preparation and sequencing. Please use this link to submit your samples.

    Users who wish to prepare their own libraries for sequencing should follow the corresponding Illumina protocol. Samples should be gel/beads-purified.

  • Submission: Users should submit 10 uL of undiluted sample (The Core will accept 2 ul for Nanodrop. If <5 ng/ul, we suggest you remake the libraries). Excess samples will be retained in our freezers for potential future re-runs. Users are also strongly encouraged to retain a portion of their samples in case of emergency.

  • Data: Images acquired from the HiSeq2000 are processed through the bundled Illumina image extraction pipeline (CASAVA) to get the sequence and quality score for each base. The data is aligned to a reference genome using an interactive ELAND algorithm. An in-depth QC report is included in the package.

  • Turnaround Time: Each HiSeq run processes 8 samples/Lanes per run, or 7 samples/Lanes plus a control/Lane. A full flowcell of sample can be run usually within two weeks of submission. Partial submissions of less than eight samples/Lanes are put into 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.

  • Data output: All of the sequencing data is stored in a Yale central server for two months. When the sequencing is complete, a link with sample information will be provided to an online website where you can click and download your data.

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 both library preparation and sequencing. Please use this link to submit your samples.

    Users who wish to prepare their own libraries for sequencing should follow the corresponding Illumina protocol. Samples should be gel/beads-purified.

  • Submission: Users should submit 10 uL of undiluted sample (The Core will accept 2 ul for Nanodrop. If <5 ng/ul, we suggest you remake the libraries). Excess samples will be retained in our freezers for potential future re-runs. Users are also strongly encouraged to retain a portion of their samples in case of emergency.

  • Data: Images acquired from the HiSeq2000 are processed through the bundled Illumina image extraction pipeline (CASAVA) to get the sequence and quality score for each base. The data is aligned to a reference genome using an interactive ELAND algorithm. An in-depth QC report is included in the package.

  • Turnaround Time: Each HiSeq run processes 8 samples/Lanes per run, or 7 samples/Lanes plus a control/Lane. A full flowcell of sample can be run usually within two weeks of submission. Partial submissions of less than eight samples/Lanes are put into 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.

  • Data output: All of the sequencing data is stored in a Yale central server for two months. When the sequencing is complete, a link with sample information will be provided to an online website where you can click and download your data.

Contact:

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
e-mail:mei.zhong@yale.edu

Location:

10 Amistad Street, Room 203
New Haven, CT 06520