CRISPR Knockdown Cell Line Protocol

Before Transduction

1. 1 day prior to transfection, seed approximately 1.0 x 10^5-3.0 x 10^5 cells in each well of a 6-well plate containing 2 mL of complete growth medium.

2. Grow cells overnight to approximately 90%-95% confluence.


1. Remove media from wells. Add 110 μl media and Hexadimethrine bromide (final concentration 8 μg/ml) to each well. Gently swirl the plate to mix. If working with a cell type for the first time, a hexadimethrine control only well should be used to determine cell sensitivity.

2. Add 2-15 μl of lentiviral particles to appropriate wells. Gently swirl the plate to mix. Incubate 18-20 hours at 37°C in a humidified incubator in an atmosphere of 5-7% CO2.

3. Remove the media containing lentiviral particles from wells. Add fresh media to a volume of 120 μl to each well.

4. Remove media from wells. Add fresh media containing puromycin.

5. Replace media with fresh puromycin containing media every 3-4 days until resistant colonies can be identified.

Single clone isolation

We recommends isolating single cells. The reason is that if you want to obtain a cell line with your gene product completely modified, single clone isolation will get rid of the cells in which the gene is either incompletely modified or that went untransfected, and that carry unwanted background mutations. Clonal isolation is followed by an expansion period to establish a new clonal cell line. Note that cell types can vary substantially in their responses to single-cell isolation, so literature specific to the cell type of interest should be consulted.

Single clone isolation method A: Cloning cylinders (recommended for adherent cells).

1. 24-48 hours after transfection, trypsinize the cells and transfer to a sterile 15 mL centrifuge tube.

2. Centrifuge the cells at 1,000 x g for 3 minutes.

3. Resuspend cell pellet in 5 mL complete growth medium.

4. Count the number of live cells in a hemocytometer to determine the cell density.Use trypan blue to exclude dead cells, which take up the dye and turn blue.

5. Dilute cells in 40 mL of complete growth medium containing antibiotic that selects for the donor plasmid in a sterile 50 mL centrifuge tube.

6. Make 4 10-fold serial dilutions from the starting.

7. Dispense 10 mL of each diluted cell suspension into each of 4 10 cm tissue culture dishes. If your transfection efficiency is low and you did not enrich for transfected cells, you will need to scale this up accordingly in order to obtain and screen more clones.

8. Incubate the plates at 37°C until cells have grown into colonies that are large enough to remove using sterile cloning cylinders, from plates carrying 10-20 colonies each. This can take several (3-6) weeks, depending on the growth rate of the parent cells.

9. Remove 20 single clones from the plates using sterile cloning cylinders. Transfer each clone to 1 well of a 24-well plate containing 0.5 mL of complete growth medium.

Single clone isolation method B: Serial dilutions (for both adherent and suspension cells). Please note that serial dilution provides no guarantee that the colonies arose from single cells. A second round is advised to increase the likelihood that clonal isolation is successful.

1. Fill each well of a 4 sterile 96-well plates with 100 μL of medium, except for well A1, which should remain empty.

2. Add 200 μL cell suspension to well A1. Mix 100 μL from A1 with the medium in well B1. Avoid bubbles. Continue this 1:2 dilution through column 1. Add 100 μL of medium back to column 1 so that wells A1 through H1 contain 200 μL.

3. Mix cells and transfer 100 μL of cells from column 1 into column 2. Mix by gently pipetting. Avoid bubbles. Repeat these 1:2 dilutions through the entire plate. Bring the final volume to 200 μL by adding 100 μL of medium to all but the last column of wells.

4. Incubate plates undisturbed at 37°C.

5. Cells will be observable via microscopy over 3 days and be ready to score in 5-8 days, depending on the growth rate of cells. Mark each well on the cover of the plate indicating which well contains a single colony. These colonies can later be subcultured from the well into larger vessels.

Clone screening

We recommends using qPCR method for clone screening.

1. Grow candidate clones to approximately 95% confluency (for adherent cells) or to a density of ~1 x 10^7 cells /mL (for suspension cells).

2. Split cells to two new plates or flasks for each candidate clone.

3. Harvest cells of each clone and extract total RNA.

4. Perform RT-qPCR to analyze the expressiom level of the target gene.

5. If the expression of the target gene reduce significantly in some single clones, the cell lines are desired.