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Sequencing Technologies and Analysis

The Sequencing Technologies and Analysis Shared Resource provides access to high throughput Next Generation Sequencing (NGS) technologies and to full service Sanger DNA sequencing using fluorescence-based technology. The Shared Resource is currently developing services to offer gene expression profiling and other genomics readouts from heterogeneous tissue samples at single-cell resolution. In combination, the Resource offers cutting-edge technology along side convenient in-house services for a broad range of genetic analysis. For more information see below or contact the Resource Director, Dick McCombie, Ph.D.

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Shared Resource Staff

NGS Project Manager

Sara Goodwin, Ph.D.
516-422-4153
sgoodwin@cshl.edu

The Woodbury Genome Center is home to the latest in both short and long read sequencing technology. Our high-throughput sequencing technology offers a broad range of applications including:

  • De novo genome sequencing/genome re-sequencing
  • Whole genome or targeted methylation analysis
  • Targeted sequencing using hybrid selection (i.e. exome and panel sequencing)
  • siRNA and small RNA sequencing
  • ChIP-Seq and RIP-Seq
  • RNA-Seq

Equipment

The facility houses a suite of Next Generation Sequencing equipment. The core currently operates one Illumina HiSeq2500, two Illumina NextSeq500s, one NextSeq 550 and one Illumina MiSeqs, which can be used to produce more than 4 trillion bases (Tb) in reads each month.

The Core also contains one Pacific Biosciences Sequel II sequencer which generates can operation in either HiFi or CLR mode. The HiFi mode generates reads 10-15kb with a yield of up to 30Gb of unique data per SMRTcell. The accuracy of the HiFi reads is greater than 99.9%. The CLR mode can generate reads in excess of 30kb and yields up to 90 Gb of unique data per SMRTcell. Run at capacity this instrument can generate >1Tb of unique data a month.

The Core also houses one Flonge, six Oxford Nanopore MinIONs, 1 Oxford Nanopore GridION and 1 Oxford Nanopore PromethION. Each platform can generate reads in excess of 100kb, with various yields. The PromethION, our highest throughput instrument, can generate up to 140Gb or >100M reads (length dependent) per cell. At full capacity the PromtheION is capable of generating >25Tb of data a month.

Please contact the Next Generation Genomics Core at nextgenseq@cshl.edu for consultation on applications, experimental set-up, strategies for experimental design, and library preparation requests.

The DNA Sequencing Shared Resource provides cost effective and rapid DNA sequence analysis using an ABI3730 instrument. The DNA Sequencing Facility offers full service fluorescent-based capillary DNA sequencing. Users can submit samples of PCR products, single and double stranded plasmids, BACs and cosmids. Facility staff set up reactions, run the samples and post final data on a shared drive for retrieval. The resource also provides consulting expertise for DNA preparation to improve the DNA sequencing results of the users. The on-site service provides convenience and a rapid turn-around time, facilitating the many projects that require DNA sequencing support.


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