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Solexa Sequencing Core

Description

The Core is built around the Illumina Solexa Genome Analyzer II.

The sequencing technology relies on the hybridization and amplification of fragments of DNA to a planar, optically transparent surface of a flow cell. A flow cell has eight lanes. One lane is always set aside for a standard control DNA. Each fragment bound to the flow cell is sequenced by synthesis using a robust four-color DNA sequencing-by-synthesis technology that employs reversible terminators with removable fluorescent dyes. Each lane is divided into two columns of 50 “tiles.” Each tile is imaged four times (once for each base) per cycle. This process generates 115,200 images for a 36-cycle run. The images are analyzed, and the analyzed data are sent to the Pipeline server for further analysis. A typical 36-cycle ChIP-seq run will produce about 200-400 million bases of aligned sequence. A paired-end run will generate twice this amount.

Timelines

  • The standard timeline to prep up to seven samples simultaneously: One to two days
  • Generation of clusters: Five hours (see the sequencing technology above.)
  • Single-read sequencing 36 bases: Up to 60 hours
  • Paired-end sequencing 36 bases: About five days
  • Data analysis: About two days

Therefore, the minimum time before results are ready is seven days.

Services Provided

36, 54 or 72 base sequencing

  • Single-read ChIP-Seq
  • Single-read methylation studies
  • Paired-end sequencing of methylation studies
  • Paired-end mRNA-Seq
  • Paired-end or Single-read Nucleosome sequencing

Sample Submission

Please contact Dr. Ramagli to schedule a time to drop off samples and discuss your project. Sample(s) must be submitted with an ESSC Sample Sheet.

Approximate Cost

  • Single-read sequencing: $1100/lane
  • Paired-end sequencing: $1750/lane

Frequently Asked Questions

Who can submit samples to the Core?

This Core primarily serves researchers at M. D. Anderson Cancer Center. It serves researchers at other Texas Medical Center institutions upon special request.

What do I submit to the Core?

Double-stranded DNA

How much does it cost?

  • Single Read: $1100/sample/lane
  • Paired-End: $1750/sample/lane

How much do I need?

  • ChIP-Seq: Minimum 10 ng, best about 50 ng
  • Genomic DNA: Minimum 100 ng, best <500 ng
  • mRNA-seq: Start with 1-10 µg total RNA and create ds cDNA < 500 ng

In what solution should the DNA be?

<30 µl of TE or 10 mM Tris HCl pH 8.5 (EB buffer)

What paperwork do I fill out?

ESSC Sample Sheet (doc)

Contact Information

The Center for Cancer Epigenetics Solexa Sequencing Core is located in the Basic Sciences Research Building, Room S9.8229.

The laboratory telephone number from inside M. D. Anderson is 7-5652.

Louis S. Ramagli, Ph.D., Lab Manager
Phone: 713-834-6299
E-mail: lramagli@mdanderson.org

Bioinformatic Collaborators

  • M. D. Anderson: Shoudan Liang, Ph.D.
    Shoudan@mdanderson.org
  • Baylor College of Medicine: Wei Li, Ph.D.
    WL1@bcm.edu
    The Computational Genomics lab at Baylor College of Medicine is focused on integrative modeling of epigenetic and transcription regulation, including:
    • transcription factor binding and histone modifications (ChIP-seq)
    • DNA methylation at single nucleotide resolution (Bisulfite-seq)
    • nucleosome remodeling (Mnase-seq)
    • alternative splicing (RNA-seq).

© 2009 The University of Texas M. D. Anderson Cancer Center