Functional Genomics and Bioinformatics Core

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).

Email Us

Learn More

Services

The major services at this core include:


  • Nucleic acid isolation, quality analysis and manipulation
  • Quantitative real-time PCR analysis
  • RNAScope
  • RNA-sequencing
  • Chromatin immunoprecipitation
  • CRISPR/Cas9 mediated genome editing
  • Coordination of high-throughput sequencing services

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


  • Gene expression and pathway analysis of microarray and RNA-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
  • 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

Publications

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.

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.

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.

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.

Meet Our Team