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Sequencing and Discovery Genomics

The Sequencing and Discovery Genomics team provides technical and collaborative support to Stowers Institute scientists who need to perform nucleic acid sequencing in the course of their research, including traditional and next-generation techniques.

Overview of Services

Research Services

Members of the Sequencing and Discovery Genomics team consult with researchers to understand their unique needs, and provide expert guidance, tools, and assistance for project completion. They also participate in cutting-edge application and technology development, and provide education and training to researchers in multiple areas of genomics.

As Stowers was one of the first institutes in the Midwest region to offer Next Generation Sequencing (NGS) through Illumina platforms, the team has extensive experience with this technology. Rapid high-throughput, short-read sequencing is offered in-house using the Illumina NGS platforms. For projects requiring long-reads, outsourcing for PacBio sequencing is offered using trusted external partners. In addition to NGS, the team performs high-throughput plasmid preparation and Sanger sequencing.

Technologies

  • lllumina NextSeq 2000
  • Illumina NextSeq 500
  • Illumina MiSeq
  • 10X Genomics Chromium Controller/iX
  • S2 Genomics Singulator
  • Logos Biosystems Luna FL Cell Counter
  • Agilent 2100 Bioanalyzers
  • Sage Science Pippin Prep/BluePippin/Pippin HT
  • Covaris S220 Focused Ultrasonicator
  • PerkinElmer Sciclone NGS Workstation
  • Beckman Coulter Biomek FXp
  • Formulatrix Mantis
  • SPT Labtech Mosquito HV
  • Thermo Fisher Scientific/ABI 3730 DNA Analyzers
  • Invitrogen Qubit Fluorometers
  • Oxford Nanopore MinION
  • Labconco CentriVap

Software and Computing

Sequencing and Discovery Genomics team works very closely with the institute's Computation Biology team for data analysis.

Team Contact

Anoja Perera

Director, Sequencing and Discovery Genomics

Stowers Institute for Medical Research

Portrait of Anoja Perera

Omics and Sequencing

Chromatin Immunoprecipitation Sequencing, or genome-wide DNA/protein interaction sequencing, DNA sequencing, whole transcriptome and single cell RNA sequencing are just some of the services we provide to Stowers scientists.

Next Generation Sequencing

The Sequencing team at the Stowers Institute began offering Next Generation Sequencing (NGS) to the Institute in September 2007 on the Illumina Genome Analyzer (GA). We have continuously updated and added sequencing instruments over the years to stay current with advances in technology and Institute demand. The current Illumina NGS sequencers available at Stowers are the NextSeq 2000, NextSeq 500 and MiSeq. We also have quick access to the NovaSeq 6000 through our neighbors at KUMC. Currently, we use Illumina sequencing systems for many different applications.

Single Cell Genomics

Interest in single cell sequencing applications has greatly increased in recent years as technologies have been developed to enable the study of heterogeneity that exists at the individual cell level. The Sequencing team offers single cell sequencing services mainly using 10X Genomics workflows.

Heatmap plot of gene expression data

Spatial Transcriptomics

The spatial organization of cells within a given tissue plays a crucial role in determining their overall function. Driven by the importance of understanding this organization, spatial transcriptomics is quickly coming to the forefront of new Next Generation Sequencing (NGS) applications with the ability to map cellular gene expression back to a specific location within the tissue. The Sequencing team has experience with two spatial transcriptomics workflows, namely Slide-seqv2 (a method published in Nature Biotech (2021) by Stickels et al) and Visium, a commercialized kit from 10X Genomics.

Sanger Sequencing

Sanger based, dye-terminator sequencing of plasmids, PCR products, BACs and Lambda DNA is performed using two ABI 3730xl 96-capillary DNA analyzers. The reactions are performed with modified versions of Applied Biosystems (Big Dye Terminator ver. 3.1) protocols. Unincorporated nucleotides are removed by exclusion columns from Edge Biosystems or by SPRI technology from Agencourt.

Automation for Sequencing

Our team members have extensive experience with automation and we have invested in cutting edge equipment to allow for processing of samples in both 96-well and 384-well format. We offer high throughput processing of samples to either feed into our Sanger Sequencing or Illumina sequencing. Often, reactions are miniaturized using specialized instruments that allow low volume pipetting to reduce costs significantly.

Featured Publications

Single-cell reconstruction with spatial context of migrating neural crest cells and their microenvironments during vertebrate head and neck formation

Morrison JA, McLennan R, Teddy JM, Scott AR, Kasemeier-Kulesa JC, Gogol MM, Kulesa PM. Development. 2021;148:dev19468. doi: 19410.11242/dev.199468.

Identification of rare, transient post-mitotic cell states that are induced by injury and required for whole-body regeneration in Schmidtea mediterranea

Benham-Pyle BW, Brewster CE, Kent AM, Mann FG, Jr., Chen S, Scott AR, Box AC, Sánchez Alvarado A. Nat Cell Biol. 2021;23:939-952.

Multiple Niche Compartments Orchestrate Stepwise Germline Stem Cell Progeny Differentiation

Tu R, Duan B, Song X, Chen S, Scott A, Hall K, Blanck J, DeGraffenreid D, Li H, Perera A, Haug J, Xie T. Curr Biol. 2021;31:827-839 e823.

Tumor-initiating stem cell shapes its microenvironment into an immunosuppressive barrier and pro-tumorigenic niche

He X, Smith SE, Chen S, Li H, Wu D, Meneses-Giles PI, Wang Y, Hembree M, Yi K, Zhao X, Guo F, Unruh JR, Maddera LE, Yu Z, Scott A, Perera A, Wang Y, Zhao C, Bae K, Box A, Haug JS, Tao F, Hu D, Hansen DM, Qian P, Saha S, Dixon D, Anant S, Zhang D, Lin EH, Sun W, Wiedemann LM, Li L. Cell Rep. 2021;36:109674.doi: 10.1016/j.celrep.2021.109674.

Prospectively Isolated Tetraspanin(+) Neoblasts Are Adult Pluripotent Stem Cells Underlying Planaria Regeneration

Zeng A, Li H, Guo L, Gao X, McKinney S, Wang Y, Yu Z, Park J, Semerad C, Ross E, Cheng LC, Davies E, Lei K, Wang W, Perera A, Hall K, Peak A, Box A, Sánchez Alvarado A. Cell. 2018;173:1593-1608.e20.

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