Open rargelaguet opened 1 year ago
Yes, that's correct.
We performed lots of experiments and analyses and found these two different conditions with different starting cell lines (hADSCs and HEFs) went through very similar trajectories towards hCiPSCs, and the Intermediate Plastic State cells at the end of Stage II also had the same features (Fig. 3, Extend Fig. 6 & 7, etc.).
However, to get higher reprogramming efficiency, these two cell lines need different additional chemicals and duration for each stage (Extend Fig. 4). HEFs can get a higher efficiency with a simpler combination of chemicals at Stage I and Stage II, so we studied the function of each chemical such as 5azac or JNKIN8 using HEFs.
Actually, those withdraw experiments were performed for both conditions and the results were the same. But we did not collect the single-cell data repeatedly.
Thanks a lot for the explanation :) I will leave this Issue open for a few days just in case I have some other questions while I reprocess the scATAC-seq data.
Hi, I am trying to download the scATAC-seq data and remap it to hg38. I just wanted to double check that I got the experimental design and sample assignments right.
You basically did scATAC-seq on two cell lines:
Is this correct? If so, can I ask why did you use different conditions and time points for the two cell lines? there is data for stage1 for hADSCs but only stage 2 for hEFs. Also, you have -5azac and -JNKIN8 for hEFs but not for hADSCs.
Thanks again! Ricard