Services and Equipment

Bioimaging:  David Burk

  1. Tissue processing and Specimen Handling:
    • Sakura VIP 6 tissue processor
    • Leica cryostats*, microtomes*, autostainer
    • Leica LMD6000 laser microdissection*
    • Miltenyi Biotec gentleMACS Octo Dissociator with heaters
  2. Immunohistochemistry / In situ staining:
    • ACD RNAScope + Hybridization oven*
    • Leica BOND Max
  3. Whole slide scanning and analysis (brightfield + fluorescence):
    • Hamamatsu NanoZoomer / Visiopharm software*;
    • Zeiss Axioscan 7, BF/POL/TIE, 5-color fluorescence
  4. Widefield Imaging (fluorescence, phase, live-cell, multi-well)*:
    • Leica DMI6000; BioTek Lionheart FX
  5. Confocal microscopy*:
    • Leica SP5; Olympus FV1000
  6. Light-sheet imagingy:
    • LaVision BioTec Ultramicroscope II, 3-laser, solvent-based tissue clearing, super-plan upgrade w/1.1x and 4x objectives
    • 3D analysis workstation*: Bitplane Imaris; syGlass VR;
  7. FACS: BD FACSCalibur*; FACSAria, Fortessa X20 (LSU-SVM):
    • 15-channel analysis, 10-channel sorting in BSL2 environment

 

Light Sheet Imaging

Light Sheet Imaging

Paraffin Sectioning

Paraffin Sectioning

Whole Slide Scanning

Whole Slide Scanning


Genomics: J. Michael Salbaum

  1. Nucleic acid measurement and Quality Control:
    • Agilent Bioanalyzer*, Nanodrop*, Qbit*
  2. Gene expression:
    • Quantitative real-time PCR, ABI QuantStudio 6 Pro (x4)*
    • BioRad Digital Droplet PCR*
    • pipetting robotics: Eppendorf epMotion 5075t, 96- & 384-well plates
  3. Next-generation sequencing: Illumina NextSeq 2000
    • Transcriptome / RNA sequencing
      • Lexogen3’-QuantSeq; Illumina mRNA-Seq, Lexogen miRNA;
      • Bioinformatics: STAR, collapse_UMI_BAM, HT-Seq, DESeq2, FactoMineR, factoextra;
    • Chromatin: ChIP-Seq; ATAC-Seq
      • Bioinformatics: GALAXY (Macs2); homer;
    • WGS or targeted Methyl-Seq; Bioinformatics: DMRSeq;
    • single cell RNA sequencing: 10xGenomics Chromium
      • Bioinformatics: Cell Ranger, Loupe Browser*; SEURAT;
    • Pathway analyses: IPA*, GSEA*, ENRICHR*, Panther*;
    • single cell / single nucleus mRNA sequencing: 10xGenomics Chromium
      • Bioinformatics:  Cell Ranger;  Loupe Cell Browser*;  SEURAT
    • Pathway analyses: IPA*, GSEA,  ENRICHR,  WebGestalt
  4. Microbiome sequencing: Illumina MiSeq, Illumina NextSeq 2000
    • 16S metagenomics, V4; (V3-V4);
      • Bioinformatics: mothur/usearch/Deseq2/PhyloSeq
    • whole genome metagenomics sequencing
      • Bioinformatics: KRAKEN2, kanju;

 

DNA Sequencing

DNA Sequencing

QuantStudio 6 Pro PCR

QuantStudio 6 Pro PCR

Robotic Pipetting Station

Robotic Pipetting Station

Digital Droplet PCR

Digital Droplet PCR


 

* user-accessible technology