CGH Protocol-Metaphase chromosome preparation

Thursday, January 29, 2004

Description
CGH is a molecular cytogenetic method of screening a tumor for genetic changes. The alterations are classified as DNA gains and losses and reveal a characteristic pattern that includes mutations at chromosomal and subchromosomal levels.

Procedure
Incubate culture for 72 hours in CO2 cell culture incubator, mix flask 1-2 times per day
Add Colcemid (about 45 min before harvesting)
Make 2 aliquots and transfer cell into 50 ml Falcon tubes
Incubate in cell cuture incubator or 37C water bath for additional 45 min
Centrifuge for 10 min at 1000 rpm
Remove supernatant e.g. with a cell culture pipettor until 5 ml remain
Gently add 40 ml KCl (0.075 M, 37C), first 5 ml drop by drop (hypotonic treatment)
Incubate for 25 min in 37C water bath
Centrifuge 10 min at 1000 rpm
remove supernatant, leave about 5 ml, resuspend pellet
Add 2 ml fixative, mix well
Add fixative until 40 ml, mix meanwhile
Repeat steps 9 - 12 until the pellet is white (at least 4 times)
After removal and resuspension of the pellet, transfer cell in 15 ml Falcon tube
Repeat steps 9 - 12, add just 10 ml fixative
Remove fixative until about 2 ml final volume
Resuspend pellet and apply suspension on slides:
Cool slides to -20C (e.g. put about 10 slides in a cuvette in the -20C freezer and keep the cuvette on ice while preparing the metaphase slides)
take one slide and moisten it by breathing from very close
either drop 50-100 l of the suspension on the slide or apply the same volume to the inclined slide (the fast draining and drying of the fluid is usually an indication for good spreading)
let the susension begin to dry (the fluid film starts to retract)
put the slide briefly in 70% acetic acid
(the acetic acid step is a washing step in particular for remowing the cytoplasm, in addition it may help for the spreading of the chromosome; the cell membranes attach to the surface of the glass slides and are disrupted by the liquid flow; the temperature difference between the cell and the glass slides may help in the disruption of the cell membranes. If the weather conditions are favorable the 70% acetic acid washing step may be omitted; in our experience the best metaphases spreads occur on dry and sunny days.

18. Air dry the chromosome slide, check for chromosome spreading and cytoplasm debris in a phase contrast lab microscope, adjust volume of fixative so that the density of nuclei/metaphases is appropriate

19. If the conditons are favorable, prepare a batch of metaphases spreads

20. Keep slide in a box at room temperature (up to about 1-2 months); metaphase spreads may be kept longer at -80C or in 70% ethanol at 4C.

21. Keep fixative with lymphcates at -20C until the preparation of new slides. Add new fixative and wash cell before the preparation of new metaphase spreads.

Recipes
RPMI 1640 medium
fetal calf serum (FCS), 20%
Colcemid (e.g. Boehringer Mannheim cell biology reagents, Best.-Nr. 295892)
cell cuture flask
Phythemaglutinin, PHA-L (Seromed, M 5030)
CO2 cell culture incubator
50 ml Nunc/Falcon tubes
15 ml Nunc/Falcon tubes
KCl (0.075 M, 0.055% ?)
Fixative (methanol/acetic acid 3 : 1)
glass microscopy slides

Amounts per 5 ml blood:
40 ml RPMI 1640 Medium
10 ml FCS (20%)
5 ml peripheral blood (anticoagulation by heparin)
1.5 ml PHA
1 cell culture flask, e.g. Falcon 250 ml
prepare up to 10 flask (1 flask will yield about 50 slides)

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CGH Protocol-Metaphase chromosome preparation