Molecular Cytogenetics

Shan Zha, M.D. Ph.D., Director

Wenxia Jiang, Ph.D., Manager

The HICCC Cytogenetics Shared Resource provides both classical cytogenetic services (i.e. karyotyping, FISH, SKY) as well as state of the art modern DNA damage and DNA repair assays (i.e. kinetic analyses of DNA damage induced foci, comet assay, sister-chromatid exchange, etc.) . There are two special functional microscopes and multifunctional analytic software in place. The Carl Zeiss Axio Imager Z2 microscope is equipped with Metafer software including MSearch, MetaCyte and AutoCapt modules and can perform automatic scanning,capture of metaphase/fluorescence imaging. The GenASIs platform installed in the Nikon Eclipse E800 microscope supports G/R/C/Q-banding, FISH, and SKY. Our full time Ph.D. scientist provides both technical assistance as well as assay development support. Limited cell culture service might be available after October, 2016, when tissue culture resource could be established. Consultation for metaphase preparation is welcomed. If you have a big experiment in mind or new to the core, please contact us for an initial consultation. Schedule microscope time and request services through iLab.

Description of Services

Cell Culture and Metaphase Preparation

  • Suspension cell culture and harvesting: add mitotic blocker (2-4hr), harvest/wash cells
  • Adherent cell culture and harvesting: add mitotic blocker (2-4hr), harvest/trypsin/wash cells
  • Metaphase preparation: Hypotonic incubation, fix/wash (4X) and 1 test drop
  • For >10 samples, please discuss with manager.

Karyotype Without Banding

  • From slides, DNA dye, scan and capture (one full slide or >10 metaphases per sample, whichever is reached first), analysis of up to 10 metaphase
  • For >10 samples, please discuss with manager.

G-banded Karyotyping

  • From slides, DNA dye, seal, scan, and capture metaphase (>10 metaphase); G-band analysis of up to 10 metaphase
  • For >10 samples, please discuss with manager. SKY scope is necessary for this analysis.

Scan and Capture Only(no staining and no analysis)

  • Preliminary scan – search the entire slide or staining area for 10x thumbnail images
  • Preliminary scan with high resolution capture – scan plus acquisition of up to 50 metaphase or the entire slide, whichever is reached first.
  • For >10 samples, please discuss with manager.

Spectral Karyotyping (SKY)

  • From slides, SKY staining, scan and capture of 10 metaphase or whole slide, whichever is reached first. SKY analysis of up to 10 metaphase.

Whole Chromosome Paint (1-2 color)

  • From slides, apply paint, scan and capture of 10 metaphase or whole slide, whichever is reached first. Analysis of up to 10 metaphase.
  • Paint available in the core for mouse chr 12, 14, X, and Y.
  • Additional probes should be discussed with the manager.
  • Analysis may be performed with user-provided paints.

Telomere FISH

  • Staining and capture only – from slides, apply paint, scan and capture up to 30 metaphase
  • Staining, capture, and analysis – includes analysis of up to 30 metaphase
  • Custom FISH probe development and analysis should be discussed with the manager. The core will label and test on one slide of human or mouse origin with a customer purchased probe

Sister Chromatid Exchange (SCE) Quantification

  • Staining and capture only – from slides, apply paint, scan and capture 10 metaphase or one slide, whichever is reached first.
  • Staining, capture and analysis - 10 metaphase or one slide, whichever is reached first.

DNA Damage Foci Quantification

  • Search and capture only or search, capture, and automatic quantification. This service can be performed independently by the user who will be charged the hourly fee for equipment use.
  • Staining, capture, and analysis of up to 30 metaphase or one slide (service performed by core staff): Start from fixed cells (grown and treated on special slide which is compatible with scanning), stain, mount with DAPI counter staining, scan, acquisition and automatic foci counting. Standard parameters are available for commonly used mouse and human cells. Current ready to use assay including (for both human and mouse cells) - Phosphorylated H2ax ; total Rad51, phosphorylated RPA (T21). Additional new antibodies will be tested in the future. For customer antibodies, please discusse with the manager.

Comet Assay (neutral or alkaline) (Trevigen comet assay based)

  • Staining, search, and capture (no analysis). Starting from cells grown on a dedicated chamber (2 wells per slide), fix, stain, scan, and capture of 5 fields.
  • For larger projects and for slides, contact the core manager.