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Core Facilities

Next-Generation Sequencing and Expression

Sujith A. Valiyaparambil and Illumina

The Next-Generation Sequencing and Expression facility, managed by Sujith A. Valiyaparambil, offers instrumentation and services — including gene expression and genome analysis — that support a variety of different experiments.

Services

This facility offers high-throughput, next-generation sequencing on two illumina HiSeq2500 and MiSeq platforms. We have expertise in whole-genome, exome, epigenetic and microbiome sequencing, and we work in conjunction with a team of bioinformaticists to help facilitate rapid analysis and algorithm deployment, as well as data storage and management.  

In addition to our deep sequencing offerings, we also provide gene expression analysis services on Affymetrix platforms, including 3’-expression, miRNA, exon and gene arrays.

Next-Generation Sequencing

Our illumina HiSeq 2500 platform supports a variety of different experiments, including whole-genome and candidate-region sequencing, transcriptome analysis, small RNA discovery, methylation profiling and protein-nucleic acid interaction analysis at a genome-wide scale. It is an excellent platform for projects that need broad coverage and can accommodate short read lengths.

Bioinformatics

Standard analysis of sequencing data generated at our facility includes FastQC quality reports and assay specific genomic alignments. 

Our analysis offerings currently include:

  • ChIP-seq: Genomic alignments through peak-calling
  • RNA-seq: Genomic alignment through differential expression
  • MiRNA: Adapter trimming and miRBase quantification
  • Whole-genome: SNP/Indel calling and structural variants (bacterial)
  • ATAC-seq: Collaborative analysis is available upon request
  • 16s Microbiome: Collaborative analysis is available upon request
  • Custom analysis for projects sequenced at our facility is available upon request

Gene Expression

Our Affymetrix Gene Chip System provides expression analysis services on all Affymetrix Gene Chips, including 3’-expression, miRNA, exon and gene arrays.

It performs sample quality analysis using the Agilent 2100 Bioanalyzer, target labeling, fragmentation, hybridization, staining and scanning.

Lab personnel conduct initial data analysis. You can arrange additional data analysis services with bioinformatics specialists at the University at Buffalo or Roswell Park Cancer Institute.

Instrumentation

  • illumina HiSeq 2500 is a flexible and scalable platform that features two run modes — rapid-run and high-output run mode — and the ability to process one or two flowcells simultaneously.
  • illumina MiSeq is a platform specializing in more targeted sequencing geared toward smaller genomes and smaller search space investigation.
  • Diagenode SX-8G Compact Automated Systems automates library preparation and immunoprecipitation steps. Our lab has demonstrated efficient and reproducible construction of RNA-seq libraries utilizing this system. 
  • QX100 Droplet Digital PCR Machine (Biorad)
  • Affymetrix Gene Chip System comprises a GeneChip Scanner 3000, two Fluidics 450 units and a GeneChip Hybridization Oven 640.

Location

UB New York State Center of Excellence in Bioinformatics and Life Sciences
Buffalo Niagara Medical Campus
701 Ellicott Street
Buffalo, NY 14203

Contact Information

Laboratory Manager

No Picture

Sujith A. Valiyaparambil

Center of Excellence in Bioinformatics and Life Sciences Lab #B3-123

701 Ellicott Street, Buffalo, NY 14203

Phone: (716) 881-7514

Email: alphy@buffalo.edu

Director

Nowak, Norma

Norma Nowak, PhD

Professor

701 Ellicott Street, Room B2-201 Ellicott Street, Center of Excellence Buffalo, NY 14203

Phone: 881-8903; 845-1698

Email: njnowak@buffalo.edu