University of Pittsburgh Cancer Institute (UPCI)

CCSG Acknowledgement

Required CCSG Acknowledgement

The NCI requires that publications acknowledge the UPCI CCSG support, and they are tracking compliance. If a UPCI CCSG-supported Shared Resource provided data used in your publication, please include the following statement in the acknowledgment section of your publication(s):

"This project used the UPCI [insert name(s) of shared resource(s)] that [is/are] supported in part by award P30CA047904."

Shared Resource Directors: Please make sure to include this statement on all of your order forms, contracts, etc. as a reminder to your users to acknowledge the UPCI CCSG support.


Genomics Services: RNA Sequencing

The CBF possesses state-of-the-art next generation sequencing equipment which employs massively parallel sequencing of small nucleic acid fragments to generate nearly complete coverage of whole genomes at greater than 99% accuracy. Unlike traditional Sanger sequencing, entire human genomes can be generated in less then 2 weeks.

The SOLiD 4 sequencer is the workhorse of our sequencing laboratory and can be used for the following applications:

  • Exome and targeted resequencing, allowing scientists to capture or target only the regions of interest of the human genome and then use high-throughput sequencing to assess the genetic variation within the captured DNA fragments.
  • Whole transcriptome analysis, allowing for conservation of strandedness of cDNA, allowing discernment between overlapping RBAs transcribed from the sense or antisense strand and multiplexing/sequencing of multiple RNA libraries simultaneously.
  • Small RNA analysis, which is a hypothesis-neutral method, provides whole genome analysis of expression patterns enabling the discovery of novel RNA without the probe bias of microarrays.
  • Chromatin immunoprecipitation sequencing (ChIP-SEQ). Sequencing of millions of ChIP-enriched DNA fragments using next generation sequencing technology enables cost-effective and precise analysis of the binding sites of transcription factors, replication and transcriptional machinery, structural proteins such as histones, as well as the impact of protein modifications on genome occupancy.

Affymetrix GeneChip Scanner 3000 7GThe Ion Torrent Personal Genome Machine is geared towards high quality, longer reads, and fast turnaround time. Specific applications include de novo viral and microbial sequencing and resequencing, as well as human scale amplicon resequencing. To find out more about the CBF sequencing capabilities or to design a study with the CBF, please contact Maureen Lyons or Patricia Petrosko.

Technology and Equipment

Life Technologies SOLiD System

Life Technologies SOLiD System

The SOLiD™ 4 System enables researchers to obtain higher-quality genomes at lower cost without the purchase of a new instrument. Benefits include:

  • Scalable system
    The SOLiD™ 4 System provides 100 GB of High Quality Genomic Sequence
  • Superior accuracy
    More than 80% of the bases have quality values >30 for higher confidence in your results
  • Uniform coverage
    Total Precision reagents improve coverage to enable the discovery of rare variants in difficult (GC/AT-rich) regions of the genome for fewer false negatives
  • Expanded application support
    Barcoded paired-end sequencing that detects somatic mutations, novel splice variation, and fusion transcripts with less input material
  • Automated sample preparation
    80% reduction in hands-on time

Ion Torrent

Ion Torrent

Ion Torrent™ uses a new sequencing technology that brings the transformative power of the semiconductor to the life sciences.

Ion Torrent™ Technology directly translates chemically encoded information (A, C, G, T) into digital information (0, 1) on a semiconductor chip. This approach marries simple chemistry to proprietary semiconductor technology – the result is a sequencing technology that is simpler, faster, more cost effective and scalable than any other technology available.