Services and Equipment

Genomics Component:  J. Michael Salbaum

1. Nucleic acid measurement and Quality Control:
  • Agilent Bioanalyzer*, Nanodrop*, Qbit*
2. Gene expression:
  • Quantitative real-time PCR, ABI AB7900 (x4)*, ABI QuantStudio*
  • BioRad digital Droplet PCR*
3. Next generation sequencing: Illumina NextSeq
  • Transcriptome / RNA sequencing
    • Lexogen3’-QuantSeq; Illumina mRNA-Seq;  Lexogen miRNA
    • Bioinformatics:  STAR / HT-Seq / DESeq2; CLC Bio; JMP Genomics
  • Chromatin: ChIP-Seq; ATAC-Seq
    • Bioinformatics:   Clc Bio; GALAXY (MACS2); homer
  • DNA methylation: Illumina targeted methyl-Seq
    • Bioinformatics:  CLCBio
  • 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:
  • 16S metagenomics, V3 (V3-V4)

Bioinformatics:  mothur / usearch / DESeq2 / PhyloSeq


 

Bioimaging Component:  David Burk

1. Tissue processing and Specimen Handling:

  • Sakura VIP 6 tissue processor
  • Leica cryostats*, microtomes*, autostainer
  • Leica LMD6000 laser microdissection*

2. Immunohistochemistry / In situ staining:

  • ACD RNAScope + Hyb oven*
  • Leica BOND Max

3. Whole slide scanning and analysis (brightfield + fluorescence):

  • Hamamatsu NanoZooomer / Visiopharm software*

4. Widefield Imaging (fluorescence, phase, live-cell, multi-well)*:

  • Leica DMI6000; BioTek Lionheart FX

5. Confocal microscopy*:

  • Leica SP5 multi-photon; Olympus FV1000

6. Light-sheet imagingy:

  • LaVision BioTec Ultramicroscope II, 3-laser, solvent-based tissue clearing
  • 3D analysis workstation; Bitplane Imaris; syGlass VR

7. FACS (analytical and sorting)*:

  • BD FACSCalibur* (3-laser); FACSAria (12-channel); Fortessa X20 (14-channel); Cytek Aurora (5-laser)

*user accessible equipment/service


COBRE Molecular Mechanisms Core Image 2