ncRNA DMS reproduction

[elkerist]

Hi! 😁

I'm trying to reproduce the result of "Zero-shot ncRNA Fitness Prediction" provided in Extended Data Fig. 1 and Extended Data Fig. 2.
But unfortunately 😔, we were unable to locate the corresponding data for RNA aptamer DMS datasets:

• Okra dataset from Zuo et al.
• Clivia dataset from Jiang et al.
• Pepper dataset from Chen et al.

Could you please provide these datasets or let us know where we can access them? Thank you very much! 😊

[Leo-T-Zang]

Same issue here.
Can anyone help?
Tag relevant people here:
@kevinhyj @prokia

[kevinhyj]

Hi @elkerist and @Leo-T-Zang,

First of all, please accept my sincere apologies for the delayed response.

Regarding the Okra, Clivia, and Pepper datasets you mentioned: these were developed by Yiyang and Xianjun Chen specifically for RNA aptamer design. At their request, we are currently unable to open-source these datasets, as they are using this data for further downstream optimization of the aptamers.

If you are looking for alternative RNA DMS datasets for your research, I highly recommend checking out NABench and RNAGym. They provide a broader range of data that could be very useful for benchmarking.

A quick personal note on the current state of the field:
While these datasets are helpful, I believe the current landscape for RNA zero-shot fitness prediction is still quite limited. The diversity of RNA types available is relatively restricted, and synthetic aptamers alone may not be the most robust metric for evaluating a model's general performance. This lack of comprehensive, high-quality benchmarks might also be a contributing factor to why platforms like NABench and RNAGym have faced challenges in the peer-review process.

Thank you for your interest and understanding!😊😊
If you have any further questions or confusion, please don't hesitate to reach out for more discussion. I'll be keeping a close eye on this thread!!!!!! 🙏

[kevinhyj]

Here are the original publications associated with these datasets. You may want to check their supplementary materials or contact the authors directly to see if the raw DMS data has been released independently:

Okra: Zuo et al. (2023), "Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA"
Pepper: Chen et al. (2019), "Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs"
Clivia: Li et al. (2023), "Large Stokes shift fluorescent RNAs for dual-emission fluorescence and bioluminescence imaging"

[Leo-T-Zang]

Thanks!!

[kevinhyj]

😊😊 Good Luck！