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

 

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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;

 

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* user-accessible technology