Molecular Cytogenetics

  • Shan Zha, MD, PhD
    • Director
  • Wenxia Jiang, PhD
    • 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 PhD scientist provides both technical assistance as well as assay development support.

Limited cell culture service might be available. Consultation for metaphase preparation is welcomed. If you have a big experiment in mind or are new to the core, please contact us for an initial consultation. 

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.

Locations and Contacts

Irving Cancer Research Center

1130 St. Nicholas Avenue, Room 605
Phone: 212-851-4934

Shan Zha, MD, PhD

Wenxia (Wendy) Jiang, PhD

User Fees and Policies

User Policies

Unassisted Use (Meta system, only available for Certified User)

  • If you are a first-time user, you must contact the manager to make arrangements for a training session.
  • After training, you can reserve microscope or workstation time through the iLab online calendar.
  • Certified independent users may use the microscopes at any available time.
  • If you are certified user, we will send you an email notice.
  • Please do NOT share your login with others, before any concerns of the manager.
  • The microscope will be blocked for maintenance/core use on Tuesday a.m. (9 a.m.-Noon) and Thursday Noon-5 p.m.), unless notified.

Assisted Use

  • Assisted use is available Monday, Wednesday and Friday, from 9:30 a.m. to 4:30 p.m.
  • Please request appointments for assisted use or training at least 2 days in advance through the iLab online calendar

Time Limit

  • Normally, you may reserve time up to two weeks in advance.
  • Each user may sign up for a maximum of 4 peak hours per day.
  • Peak hours are Monday through Friday, 9:00 a.m. to 5:00 p.m. 
  • If you have a special need to reserve a longer period, please contact the manager.


  • If you’re more than 30 minutes late and you haven’t given us advance notice, anyone may take over your time slot.
  • If you use 20 minutes longer than the time period you reserve, you will be charged 1 hour more.
  • If you need to cancel, please do so at least 24 hours in advance.
  • If you cancel on the day of your appointment, you will be charged for any time that is not used by others.
  • Due to the significant time needed for initiation, the core microscope is not available for short time checking of staining

Data Storage

  • Data storage is free for up to 3 weeks on the scanning microscope and 4 weeks on the workstation.
  • Older data might be removed to free precious storage spaces.

User Fees

Service Rate Member Rate External Rate
Suspension cell culture and harvesting $33 $30 $36
Adherent cell culture and harvesting $55 $50 $60
Metaphase preparation $132 $120 $144
Giemsa stain karyotyping without banding ‐Staining/capture $55 $50 $60
Giemsa stain karyotyping without banding ‐Staining/capture/analysis $155 $160 $180
G‐banded karyotyping (only human) $330 $300 $360
Spectral Karyotyping (SKY) for mouse $715 $650 $780
Spectral Karyotyping (SKY) for human $605 $550 $660
Whole chromosome paint ‐ Staining/capture (paint mouse chromosome 12, 14, 15, X, Y) $220 $200 $240
Whole chromosome paint ‐ Staining/capture (user provides paint) $220


Telomere FISH ‐Staining/capture, <5 samples $220


Telomere FISH ‐Staining/capture/analysis, <5 samples $330 $300 $360
Telomere FISH ‐Staining/capture, ≥5 samples $165 $150 $180
Telomere FISH ‐Staining/capture/analysis, ≥5 samples $275 $250 $300
Custom FISH probe labeling/test $275 $250 $300
Custom FISH ‐Staining/capture (user provids probe) $275 $250 $300
Sister chromatid exchange (SCE) ‐Staining/capture $275 $250 $300
Sister chromatid exchange (SCE) ‐Staining/capture/analysis $385 $350 $420
DNA damage foci quantification ‐ Staining/capture/data export (user provids Ab) $385 $350 $420
Comet assay ‐ Staining/search/capture $385 $350 $420
Capture and scan: preliminary scan $77 $70 $84
Capture and scan: preliminary scan/high resolution $165 $150 $180
Metasystem Acquisition Station ‐ initial use and training $110 $100 $120
Metasystem Acquisition Station ‐ assisted use $88 $80 $96
Metasystem Acquisition Station ‐ unassisted use peak hours $60.50 $55 $66
Metasystem Acquisition Station ‐ unassisted use non‐peak hours $49.50 $45 $54
Metasystem Analytic Workstation ‐ initial use and training $88 $80 $96
Metasystem Analytic Workstation ‐assisted use $55 $50 $60
Metasystem Analytic Workstation ‐ unassisted use peaks hours $27.50 $25 $30
Metasystem Analytic Workstation ‐ unassisted use non‐peak hours $27.50 $25 $30
Illumina MiSeq Sequencer Self‐use $220 $200 $240


Online Reservations

The HICCC Cytogenetics Shared Resource uses the iLab Core Management System for service requests and billing. Before you can request services, you must log into iLab and be approved as a lab member.