scATAC-seq data questions

[rargelaguet]

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.

GSM5387804  scATAC-Seq fibroblast
GSM5387805  scATAC-Seq StageII
GSM5387806  scATAC-Seq StageII-5azac
GSM5387807  scATAC-Seq StageII-JNKIN8
GSM5683314  scATAC-Seq hADSCs-0618
GSM5683315  scATAC-Seq StageI-0618
GSM5683316  scATAC-Seq StageII-0618

You basically did scATAC-seq on two cell lines:

• hEFs: at stage 0 (GSM5387804), at stage II (GSM5387805), at stage II without 5azac (GSM5387806), at stage II without JNKIN8 (GSM5387807)
• hADSC: at stage 0 (GSM5683314), at stage I (GSM5683315), at stage II (GSM5683316)

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

[sajuukLyu]

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.

[rargelaguet]

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.