• Impermeant
• AT-selective
• High-affinity DNA binding

A3568 ‡ Acridine orange

500/526 (DNA)

460/650 (RNA)

• Permeant
• RNA/DNA discrimination measurements
• Lysosome labeling
• Flow cytometry
• Cell-cycle studies

• Weakly permeant
• GC-selective
• Flow cytometry
• Chromosome banding

• Chromosome banding

• AT-selective
• Alternative to quinacrine for chromosome Q banding
• Membrane phenomena

D3571

D21490 DAPI 358/461 Blue

• Semi-permeant
• AT-selective
• Cell-cycle studies
• Mycoplasma detection
• Chromosome and nuclei counterstain
• Chromosome banding

D11347

D23107 Dihydroethidium 518/605 Red §

• Permeant
• Blue fluorescent until oxidized to ethidium

• Impermeant
• dsDNA intercalator
• Dead-cell stain
• Chromosome counterstain
• Electrophoresis
• Flow cytometry
• Argon-ion laser excitable

• Impermeant
• High-affinity DNA labeling
• Dead-cell stain
• Electrophoresis prestain
• Argon-ion and green He-Ne laser excitable

• Impermeant
• Very high-affinity DNA labeling
• Electrophoresis prestain

(unbound)** Red

• Impermeant
• Photocrosslinkable
• Compatible with fixation procedures

• Permeant, except gram-negative bacteria
• Stains nuclei and cytoplasm of eukaryotes and some bacteria

H3569 ‡

H21491 Hoechst 33258 (bis-benzimide) 352/461 Blue

• Permeant
• AT-selective
• Minor groove–binding
• dsDNA-selective binding
• Cell-cycle studies
• Chromosome and nuclear counterstain

H3570 ‡

H21492 Hoechst 33342 350/461 Blue

• Permeant
• AT-selective
• Minor groove–binding
• dsDNA-selective binding
• Cell-cycle studies
• Chromosome and nuclear counterstain

• Permeant
• AT-selective
• Minor groove–binding
• dsDNA-selective binding
• Cell-cycle studies
• Chromosome and nuclear counterstain

• AT-selective
• Spectra dependent on secondary structure and sequence
• RNA/DNA discrimination
• Nuclear stain in tissue

543/712 (DNA)

590/607 (RNA)

• Permeant
• High Stokes shift
• Long-wavelength spectra
• Flow cytometry

• Impermeant
• Nuclear counterstain

P3566 ‡

P21493 Propidium iodide (PI) 530/625 Red

• Impermeant
• Dead-cell stain
• Chromosome and nuclear counterstain

* Excitation (Ex) and emission (Em) maxima in nm.
All excitation and emission maxima were determined for dyes bound to double-stranded calf thymus DNA in aqueous solution, unless otherwise indicated.

† Indication of dyes as “permeant” or “impermeant” are for the most common applications; permeability to cell membranes may vary considerably with the cell type, dye concentrations and other staining conditions.

‡ Available in aqueous solution for those wishing to avoid potentially hazardous and mutagenic powders. § After oxidation to ethidium. ** Prior to photolysis; after photolysis the spectra of the dye/DNA complexes are similar to those of ethidium bromide–DNA complexes.

2. The following day, dilute 50μl of each Excellgen KOSM-adenovirus in 4ml complete culture medium.

3. Aspirate medium from 10cm dishes and add diluted virus (4ml) to cells. Return dishes to a CO2 incubator for one hour.

4. Aspirate virus-containing medium, and replenish with 10ml iPSC medium.

5. Change medium every 48 hours.

6. Repeat adenoviral gene transduction every other 5 days as transgene expression by adenovirus will only last 5~7 days, depending on the rate of cell division. Longer expression can be expected for cells with slower cell dividing rates.

7. Wait for 2-4 weeks for iPSC colonies to form.

8. Once iPSC colonies form, prepare Mytomycin C treated MEF (mouse embryonic fibroblasts) feeder cells in a 24-well plate (80% confluent) at a concentration of 10μg/ml for 3 hours in an incubator at 37°C followed by 2X PBS wash.

9. Pick colonies manually into 96-well plate and trypsinize in 96-well plate.

10. Transfer the trypsinized cells from each of the 96 wells into 24-well MEF coated plate.

11. Wait for another 1-2 weeks for iPSC colonies to develop (change medium every 48 hours)

12. When MEF cells become too old (about 2 weeks) or a lot of iPSC colonies have developed in the 24-well plate, prepare MEF feeder layer as described above in 6-well plate to expand.

13. Trypsinize the cells (both MEF and iPSC cells) and spin down at 1000Xg.

14. Seed iPSCs into 6-well MEF coated plate for expansion.

15. Using the same procedures above, iPSCs can be further expanded to bigger culture vessels to meet your lab needs for iPSC analysis or down-stream applition

1. The day before beginning your experiment, coat a 15 cm cell culture dish with 0.2% gelatin sterile filtered in ddH₂O. Incubate the plate overnight at 37°C and 5% CO₂.
2. Aspirate the liquid from the gelatin coated dish, and seed MEF cells (we used Nanog-GFP/rtTA MEF cells) at a density of 4×10⁵
   cells per dish. Incubate the cells in 30 ml of MEF growth medium (450ml
   DMEM supplemented with 50 ml FBS, 5 ml 100x non-essential amino acids,
   5 ml penicillin/streptomycin, 5 ml 200 mM L-glutamine and 0.5 ml 55mM
   β-mercaptoethanol) for two days at 37°C and 5% CO₂ until approximately 80% confluent.
3. Aspirate the medium and add 30 ml of MEF growth medium supplemented
   with concentrated lentivirus (4 x 100 μl virus stock solution + 29.6 ml
   growth medium). Rock the dish gently to ensure even distribution of the
   medium. Incubate the cells overnight at 37°C and 5% CO₂.

2. Doxycycline Induced Reprogramming

1. 20-24 hours post-transduction, trypsinize the transduced cells,
   centrifuge at 200 x g for 5 minutes and resuspend in ES/iPS growth
   medium (450 ml Knockout DMEM supplemented with 50ml ES cell-qualified
   calf serum, 5 ml penicillin/streptomycin, 5 ml 200 mM L-glutamine, 0.5
   ml β-mercaptoethanol and 25 μl LIF) . Seed transduced MEF’s at an
   appropriate concentration for the cell culture dish size (we used 2.5 x
   10⁵ cells per 10 cm dish for reprogramming efficiency experiments and colony isolation, and 2 x 10⁴ cells per well in 4 well plates for ICC experiments). Incubate overnight at 37°C and 5% CO₂. Note: any remaining transduced cells can be frozen in liquid nitrogen for future analysis.
2. Aspirate the medium and replace with ES/iPS medium prepared fresh
   and supplemented with doxycycline to a final concentration of 2 μg/ml
   (we also added medium without DOX as a negative control). Incubate at
   37°C and 5% CO₂.

3. Immunocytochemical Analysis of Transduction Efficiency

48 hours post-doxycycline induction, determine
transduction efficiency by immunohistochemistry(ICC). Carry out ICC
testing on cells replated in 4 well plates. All volumes listed in the
following protocol should be adjusted according to the cell culture
plate size.

1. Wash the cells gently once with PBS (without Mg²⁺+ or Ca²⁺).
2. Fix the cells with 500 μl of 0.5 ml 4% paraformaldehyde in PBS for 15 minutes at room temperature.
3. Wash the cells gently two times with PBS.
4. Permeabilize cells by adding 500 μl of ice-cold 0.2% Tween®-20 in PBS. Incubate for 10 minutes at room temperature.
5. Wash the cells gently two times with PBS.
6. Block non-specific binding with 200 μl blocking buffer for one hour at room temperature.
7. Incubate the cells with 200 μl of the specific primary antibody overnight at 4°C (we used Oct4, Klf4, Sox2 and c-Myc).
8. Wash the cells gently two times with PBS.
9. Incubate the cells with 200 μl of secondary antibody for 1 hour at
   room temperature, protecting the plates from light (we used Donkey
   anti-Rabbit Rhodamine conjugate, Donkey anti-Goat AlexaFluor® 594
   conjugate, Donkey anti-Mouse Rhodamine conjugate and Donkey anti-Rabbit
   Rhodamine conjugate).
10. Wash the cells gently two times with PBS.
11. Add DAPI (final concentration 2 μg/ml in PBS) and incubate 10 minutes to visualize nuclei.
12. Wash the cells gently with PBS.
13. Add anti-fade Aqua-Mount before imaging using an inverted fluorescent microscope.

4. Isolating and expanding iPS Cell Colonies

1. After initiating the reprogramming process (as described in section
   2), monitor the cultures and replace medium every 48 hours. We used
   doxycycline containing medium to culture the cells for the first twelve
   days and then subsequently removed doxycycline from the medium to
   ensure that the iPS colonies manually picked for expansion would be DOX
   independent.
2. Cells should be monitored daily for morphological changes
   indicative of the reprogramming process; or when using cells like
   Nanog-GFP/rtTA MEF, monitor morphology and GFP fluorescence to identify
   reprogrammed colonies. Each experiment will be different, but colonies
   are generally large enough for isolation between 16 and 22 days.
   Colonies identified during this time frame can then be manually
   isolated and trypsinized for expansion and analysis.
3. The day before isolating and trypsinizing the reprogrammed
   colonies, prepare a 24-well plate by seeding with gamma-irradiated
   feeder layer MEFs at a density of 5 x 10⁴ cells per well. Incubate overnight at 37°C and 5% CO₂.
4. Manually pick each iPS colony and trypsinize to dissociate the cell
   aggregates. Re-plate the iPS cells in ES/iPS medium in individual wells
   of the 24-well plate pre-seeded with gamma-irradiated feeder layer
   MEFs. Wells should be seeded at a density of 2 x 10⁵ cells/well. Incubate at 37°C and 5% CO₂. Change media every 24 hours.
5. Monitor iPS colonies daily for growth and GFP fluorescence. We incubate our cultures for 6 days before passaging.
6. Determine which wells of the 24-well plate are uniformly expressing
   GFP. Wells that have good GFP expression can be trypsinized and
   passaged 1:8 into 4-well plates that have been pre-seeded with
   gamma-irradiated feeder layer MEFs. These plates can be used for
   pluripotent marker analysis by ICC and AP staining.

5. Immunocytochemical Analysis for Pluripotency

ICC testing is carried out on cells expanded in
4 well plates. All volumes listed in the following protocol should be
adjusted according to the cell culture plate size.

1. Wash the cells gently twice with PBS (without Mg²⁺+ or Ca²⁺).
2. Incubate in 0.5 ml of ice-cold 0.2 % Tween 20 in PBS per well for 10 minutes.
3. Wash the cells gently three times with PBS.
4. Block non-specific binding with 200 μl blocking buffer for one hour at room temperature.
5. Incubate the cells with 200 μl of the specific primary antibody overnight at 4°C (we used SSEA-1, Nanog and Oct4).
6. Wash the cells gently two times with PBS.
7. Incubate the cells with 200 μl of secondary antibody for 1 hour at
   room temperature, keeping away from light (we used Donkey anti-Mouse
   Rhodamine conjugate and Donkey anti-Rabbit Rhodamine conjugate).
8. Wash the cells gently two times with PBS.
9. Add DAPI (final concentration 2 μg/ml in PBS) and incubate 10 minutes to visualize nuclei.
10. Wash the cells gently with PBS
11. Add anti-fade Aqua-Mount before imaging using an inverted fluorescent microscope.

6. Alkaline Phosphatase (AP) Staining of iPS Cell Colonies

1. iPS colonies from section 4 can also be analyzed for AP activity
   utilizing commercially available kits and following the manufacturer’s
   protocol.

Part 7. Representative Results

The DOX Inducible Mouse TF Lentivirus Kit can
be used to reprogram MEFs to iPS cells. After transduction of the MEFs,
expression of transcription factors Oct4, Sox2, Klf4 and c-Myc can be
detected in cells treated with doxycycline (DOX+), but little or no
expression can be detected in untreated (DOX-) cells . Morphological
changes will progress over time (12 days of DOX treatment in this
example) to generate larger, more ES cell-like colonies with defined
colony edges and three dimensional growth. When DOX is removed, there
is a noticeable reversion of cellular morphology for some ES cell-like
colonies, however, many of the colonies maintained their iPS morphology
(figure 2a). These iPS colonies, when picked and passaged, display
typical pluripotency marker expression of Alkaline Phosphatase (AP),
Nanog, Oct4 and SSEA-1. The type of MEF cells used in this experiment
(Nanog-GFP/rtTA MEF cells) express GFP from the endogenous Nanog locus
when reprogrammed to the pluripotency state. GFP expression can
therefore be used as a preliminary indicator for successful
reprogramming.

Source: http://biosettia.com

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http://www.nature.com/nature/journal/v481/n7381/fig_tab/nature10761_T1.html