Functional Genomics and Bioinformatics Core

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Genomics and Bioinformatics Expertise

The Functional Genomics and Bioinformatics Core, formerly known as Molecular Biology Core, provides a centralized resource for functional genomics and bioinformatic studies including expertise, equipment, and technical capabilities. The infrastructure and technical expertise is primarily to support methods in molecular, functional genomics and bioinformatics studies.

The Functional Genomics and Bioinformatics Core is supported by the Center for Pediatric Research (NIGMS CoBRE NIH P20GM103620).

Team photo inside lab

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Services

The major services at this core include:


  • Nucleic acid isolation, quality analysis and manipulation
  • Quantitative real-time PCR analysis
  • RNAScope
  • RNA-sequencing
  • Single cell analysis including single cell RNA-seq
  • Chromatin immunoprecipitation
  • Chromium X single cell analysis
  • CRISPR/Cas9 mediated genome editing
  • Coordination of high-throughput sequencing services
  • Visium Cyt Assist

Bioinformatics Support The Functional Genomics and Bioinformatics Core provides bioinformatics support such as:


  • Gene expression and pathway analysis of microarray and RNA-seq data, RNA-seq, and scRNA-seq data
  • Comprehensive analysis of ChiP-seq data including motif annotation and differential binding between conditions
  • DNAseq data analysis including Whole genome and whole exome (WGS) and (WES)

Equipment

  • Q700 Sonicator
  • 10X Chromium Controller
  • Precellys24 tissue homogenizer with Cryolys cooling unit
  • Benchmark BeadBug homogenizer
  • Promega Maxwell 16 MDx instrument for nucleic acid extraction
  • Qiacube for nucleic acid extraction
  • Life Technologies Bench Pro 2100 plasmid purification station
  • Thermo Savant SPD111V SpeedVac
  • GE NanoVue Spectrophotometer
  • Thermo ND-200 Spectrophotometer
  • Thermo NanoDrop Lite Spectrophotometer
  • Epoch Take 3 Plate Reader/Spectrophotometer
  • Agilent 2100 Bioanalyzer
  • Eppendorf Mixmate Microplate Shakers
  • Eppendorf ThermoMixer F0.5/F1.5/F2.0 (2X)
  • BioRad MyCycler 96 well Gradient Thermal Cycler (2X)
  • GeneAmp PCR system 9700 (2X)
  • Strategene MX3005p QPCR real-time PCR system
  • Applied Biosystems 7500 real-time PCR system 
  • UVP BioSPectrum 500 Imaging System
  • UVP GelDocIt 310 Imaging System
  • Beacon Designer 7 software package
  • Vector NTI Advanced Software
  • Visium CytAssist
  • Chromium X
  • CFX Opus Real-time PCR system

Publications

Anderson R, Sochacki K, Vuppula H, Scott B, Bailey E, Schultz M, Kerkvliet J, Taraska J, Hoppe A, Francis K. (2021). Cell Rep. Nov 16; 37 (7). PMID:34788623

Grausam KB, Dooyema SD, Bihannic L, Premathilake H, Morrissy AS, Forget A, et al. ATOH1 promotes leptomeningeal dissemination and metastasis of Sonic Hedgehog subgroup medulloblastomas. Cancer research. 2017.

Grassmeyer J, Mukherjee M, deRiso J, Hettinger C, Bailey M, Sinha S, et al. Elf5 is a principal cell lineage specific transcription factor in the kidney that contributes to Aqp2 and Avpr2 gene expression. Developmental biology. 2017;424(1):77-89. PMID:28215940. PMCID:PMC5382981.

Li L, Grausam KB, Wang J, Lun MP, Ohli J, Lidov HG, et al. Sonic Hedgehog promotes proliferation of Notch-dependent monociliated choroid plexus tumour cells. Nature cell biology. 2016;18(4):418-30.

Mdaki KS, Larsen TD, Wachal AL, Schimelpfenig MD, Weaver LJ, Dooyema SD, et al. Maternal high-fat diet impairs cardiac function in offspring of diabetic pregnancy through metabolic stress and mitochondrial dysfunction. Am J Physiol Heart Circ Physiol. 2016;310(6):H681-92.

Mukherjee M, deRiso J, Otterpohl K, Ratnayake I, Kota D, Ahrenkiel P, Chandrasekar I, Surendran K. Endogenous Notch Signaling in Adult Kidneys Maintains Segment-Specific Epithelial Cell Types of the Distal Tubules and Collecting Ducts to Ensure Water Homeostasis. J Am Soc Nephrol. 2019 Jan;30(1):110-126. PMID: 30514723, PMCID:PMC6317606.

Sengupta S, Yaeger JDW, Schultz MM, Francis KR. 2024. Dishevelled localization and function are differentially regulated by structurally distinct sterols. bioRxiv. 2024.05.14.593701; doi: https://doi.org/10.1101/2024.05.14.593701.

Torres H, VanCleave A, Vollmer M, Callahan D, Smithback A, Conn J, Rodezno-Antunes T, Gao Z, Cao Y, Afeworki Y, #Tao J. Selective Targeting of Class I Histone Deacetylases in a Model of Human Osteosarcoma. Cancers (Basel), 2021 Aug 20;13(16):4199. PMCID: PMC8394112

Torres, H., VanCleave, A., Rodezno T., Cao Y., Tecleab Y., Mukherjee M., Westendorf J., and Tao, J*. A preclinical study on a murine model associated with LMS. J Bone Miner Res. 2022 Feb; Volume 37; Number S1, pp. S219. https://doi.org/10.1002/jbmr.4515

Voigt, E., Walenburg, M., Wollenzien, H., Thompson, E., Kumar, K. Feiner, J., McNally, M., Friesen, H., Mukherjee, M., Afeworki, Y., Kareta, M.S. Sox2 is an oncogenic driver of small cell lung cancer and promotes the classic neuroendocrine subtype. Molecular Cancer Research, 19(12), 2015-2025 (2021)

Zylla, J. S., Hoffman, M. M. Plesselova, S., Bhattacharya, S., Calar, K., Afeworki, Y., de la Puente, P., Gnimpieba, E. Z., Miskimins, W. K., & Messerli, S. M. (2022). Reduction of Metastasis via Epigenetic Modulation in a Murine Model of Metastatic Triple Negative Breast Cancer (TNBC), Cancers,14, 1753https://doi.org/10.3390/cancers14071753

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Meet Our Team

Kamesh Surendran, PhD

Co-Director

Dr. Surendran has extensive experience with studies examining gene expression, transcriptional regulation and function of signaling pathways using genetic approaches. His research is focused on understanding the molecular regulators of kidney development.

Michael Kareta, PhD

Co-Director

Dr. Kareta has broad-ranging experience in the use of genomic assays to investigate multiple cellular mechanisms. Additionally, he is trained in the bioinformatic analysis of large datasets with the goal of incorporating genomic data to explain biological processes. His research is focused on the function of master regulators of cell fate, and how their misregulation can lead to diseases, such as cancer.

Malini Mukherjee, PhD

Core Manager

Dr. Mukherjee is a staff scientist who manages and performs the functional genomics services of the core. She has extensive experience in molecular techniques including nucleic acid isolation and manipulation, quantitative PCR, design and generation of promoter constructs, and chromatin immunoprecipitation assays. Most recently, she has utilized CRISPR/Cas9 for genome editing of cell lines.

Ben Derenge, BS

Associate Data Analyst

Ben graduated from South Dakota State University in 2020 with a bachelor's degree in Data Science and a bachelor's degree in Mathematics.

As a graduate student, Ben contributed to the development of open-source software such as IDEP, a tool for extensive analysis of RNA-sequencing data.

Ben is experienced in web development, data preparation, and various statistical modeling methods. He currently works with the Biostatistics Core and the Genomics Core.

Oduduabasi Isaiah, MS

Associate Biostatistician

Associate Biostatistician at Sanford Research, working with the Sanford Genetics and Genomics Group. I hold a Master's in Biostatistics and a bachelor's in chemical engineering. My current work primarily focuses on RNA-seq and single-cell RNA sequencing (scRNA-seq), Proteomics and pathway analysis utilizing advanced bioinformatics tools like DESeq2, Monocle3, DAVID, and Seurat to analyze and interpret genomic data. I have a passion for continuous learning and am hoping  to expand my expertise further in the genetics field.