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:
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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
