Functional Genomics and Bioinformatics Core

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
• 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, 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)

• 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

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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. 

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.