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High Throughput Genome Center

Depathment of Pathology

School of Medicine

University of Pittsburgh


SERVICES

As the record shown, even though Illumina sequencing has been increasingly used as the tool for nucleic acid quantification and polymorphism detection, Affymetrix array system remains one of the major tools for genome copy number quantification and gene expression analyses, due to its effortless nature in data output and genome mapping process. However, we foresee a significant increase in utilization of Illumina sequencing and long-read sequencing platform in the future when analysis software becomes more accurate, and the flow of data are more efficient.


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AFFYMETRIX ARRAY

Genotype analyses

  • Affymetrix SNP 6.0 array for whole genome copy number and SNP analyses
  • CytoscanHD array analysis for whole genome copy number, SNP, cytogenetic and other structural variation analyses
  • OncoScan array for copy number analyses for FFPE tissue

Transcriptome profile analyses

  • GeneChip Expression Profiling Arrays & Assays including Human, Mouse, Rat, Non-human primate, Microorganism & insect, Livestock, Bird & fish, Small mammal, Plant
  • miRNA profiling array




ILLUMINA HiSeq 2500

  • Whole genome sequencing
  • Whole genome bisulfite methylated DNA analysis
  • Transcriptome sequencing
  • Exome sequencing
  • Single cell sequencing in conjunction of 10x Genomics
  • Single cell copy number analysis in conjunction of 10x Genomics
  • ChIP or ATAC or other targeted sequencing
  • Microbiome sequencing
  • Micro RNA sequencing



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OXFORD NANOPORE

  • Whole genome sequencing for de novo assembly, structural variation, single nucleotide variation and resequencing analyses
  • Transcriptome sequencing for RNA isofrom and fusion transcript analyses using direct RNA sequencing and ligation sequencing
  • Targeted sequencing include amplicons, sequence capture and exome
  • Epigenetic sequencing including methylation, histone modification and non-coding RNA activity
  • Microbiome sequencing




SAMPLE PREPARATION

If you need our service, please fill in the Requisition Form for Affymetrix or Sequencing, and send inquiry to Dr. Jianhua Luo at luoj@upmc.edu.


Affymetrix Platform:

  • DNA analysis: genome DNA, tissues or cells pellets are acceptable
  • RNA analysis: Tissues and cell pellets are preferred. For old versions of genechip analysis, total RNA without going through RNAeasy purification is not acceptable.
  • miRNA analysis: miRNA, tissues and cell pellets are acceptable

Illumina Sequencing Platform:

  • DNA analysis: whole genome DNA, tissues, or cell pellets are acceptable
  • RNA analysis: total RNA, tissues or cell pellets are acceptable
  • Epigenomic analysis: targeted DNA fragments are acceptable

Oxford Nanopore Sequencing Platform:

  • DNA analysis: genome DNA, tissues or cells pellets are acceptable
  • RNA analysis: for direct RNA sequencing, cell pellet or tissues are preferred. Total RNA may be acceptable if freshly prepared, and for cDNA ligation sequencing, total RNA, tissues and cell pellets are acceptable.
  • Epigenomic analysis: targeted DNA fragments are acceptable.