Allen Cell Discussion Forum

Have you guys began hiPSC differentiation in to cardiomyocytes?


Have you guys began hiPSC differentiation in to cardiomyocytes?


Yes! Our method at the Allen Institute for Cell Science was adapted from the small molecule protocol described in Lian et al., Nature Protocols, 2013, and has been optimized for the differentiation of cardiomyocytes in a 6-well format using the Allen Cell Collection, derived from the hiPSC WTC parental line released by the Conklin Laboratory at the J. David Gladstone Institute.

Check out our SOP: Cardiomyocyte differentiation methods v1.0.pdf for more details!

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From the Allen Cell Collection, MYL7-mEGFP cell line, Day 12 after differentiation single_plane_image


You can also find our methods video where we set up hiPSCs for cardiac differentiation here:

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Hi, I’m just starting the Cardiomyocyte differentiation using the Allen Institute protocol. Currently at day 8 of differentiation and I’m starting to see some isolated beating clusters. I noticed that in the protocol the expected result was that there will be uniform beating across the entire well.

Would you happen to know when this uniform beating usually occur? If I don’t see uniform beating by the designated day, does that mean my differentiation failed?



We usually expect to see variation on when beating should begin between experiments, but around day 7 to day 9 you should see specific areas of the well beating. In our experience, by day 12 we usually see uniform beating across the well in experiments where the differentiation was optimal.

Please keep in mind that optimization of our protocol may be required to account for variation between cell lines. A good place to start would be varying the initial stem cell seeding density (we find that between 125k-250k cells/well in a 6wp is a good range to test).

We would suggest collecting your cells and running a flow experiment to determine the percent of cells that are troponin positive (cTnT+), which should give you a quantitative result on how successful your differentiation was.

Let me know if you have any more questions!


Hi, thank you for your response.

I ran the flow on these cells and got a very low cTnT + percentage (< 1%). I want to optimize the protocol further, do you suggest increasing or decreasing the CHIR concentration? Additionally, should I keep the IWP2 concentration at an equal ratio to the CHIR concentration?




Sorry to hear your differentiations are not working.

Would you mind providing me with some more information on the cell line you are using? In particular, are you using one of our lines and does the line you are using have good stem cell morphology? (see Pictures of Healthy vs Unhealthy hiPSC colonies for examples). Could you post an example of how your stem cells look if they do not look similar to the pictures we have provided?

Although we do see variations in cTnT+ levels between our lines and from differentiation experiments, <1% cTnT+ is extremely low for a well with beating clusters and below the range we see even in subpar differentiations at day 12 using this protocol. Have you validated your flow protocol for staining and detecting cTnT in cardiomyocytes?

We have a video on our website showing our differentiation setups ( We have found that the timing of the media changes is important. Have you been changing the media from Chiron to IWP and IWP to B27- as close to 48hrs as possible?

If so, because your cTnT+ is so low my first suspicion would be that potentially something is off with one of the reagents. We lot test our B27 minus insulin. We have found that lot to lot variations can lead to unsuccessful differentiations. Have you tested multiple B27 minus insulin lots in a controlled experiment?




Hi Haseeb, thank you for the reply.

The line I’m using is a patient-derived iPSC line that we reprogrammed ourselves here in the lab. I didn’t use the same line that you are using. They have good morphology prior to differentiation (no cratering, no spontaneous differentiating regions) and are kept at 70-80% confluency prior to routine passaging.

I’m unsure if it’s the flow protocol or the differentiation protocol that’s the issue, because I saw beating clusters on the edges of the plate and there was no beating cells in the middle at all. I timed the media changes from Chiron supplemented media to IWP2 media as close to 48 hrs as possible, and I’ve used the flow protocol before to detect cTNT+ cells derived using a commercial differentiation kit and they were able to detect cTNT+ cells.

if it’s not too much trouble, could you share the flow protocol used by Allen Cell to evaluate differentiation efficiency?

Thank you!


Hi @hwidyastuti

We do have a protocol for troponin-T staining of fixed cells (fixed in 4%PFA/PBS for 10 min). The steps are as follows:

Flow Cytometry Prep

  • In round bottom 96 well plate, plate 2 wells per sample, 80-100ul cell suspension/well.
  • Spin down at 200g, 3min, 25C (radius=15.1)
  • Flick off supernatant
  • Resuspend pellets in 99.5ul BD Perm/Wash + 0.5ul anti-Troponin T AF647 or isotype control
  • Incubate at room temperature in dark for 30min
  • Add 100ul BD Perm/Wash to wells
  • Spin down at 200g, 3min, 25C
  • Flick off supernatant
  • Add 200ul BD Perm/Wash, pipette gently 5x. Spin down at 200g, 3min, 25C. Flick off sup’t.
  • Add 200ul PBS/5%FBS, pipette gently 5x. Spin down at 200g, 3min, 25C. Flick off sup’t.
  • Add 200ul PBS/5%FBS, pipette gently 5x. Spin down at 200g, 3min, 25C. Flick off sup’t.*
  • Resuspend pellets in 200ul PBS/5%FBS+DAPI(1:1000), filter with 35um mesh cap into FACS tubes for acquisition.

We use the BD FACS AriaIII for sorting. Please let us know if you have further questions! Happy to help.


Hi Haseeb,

Thank you for the protocol! I’ve had some success differentiating commercial iPSC lines using your protocol (>97% cTNT+). I’m currently working on a patient line and I’ve identified a seeding density at which they would produce beating clusters but the beatings are localized on the periphery. I suspect I would only get less than 50% cTNT+ cells.

What do you suggest I should do next? Should I increase the Chiron concentration or change the seeding density?

Thank you! I really appreciate all your help with this.


@hwidyastuti We haven’t worked with disease lines ourselves, which we know can be a bit more finicky. However, we will in the near future, and would love to know if you gave your suggestion a try and if it worked.