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JackieHanLab / SenCID

Senescent Cell Identification
MIT License
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Can we apply SenCID to 10X Genomics sc-RNA seq? #14

Closed seasonzhao closed 3 weeks ago

seasonzhao commented 1 month ago

Our analysis re- veals that the BTD-trained SenCID is applicable to both Dropseq- (Figures 2A, 2C, 2D, and 2F) and Smart-seq- (Figure 2B) generated single-cell data.

Is there any difference between 10X, Dropseq and Smart-seq? Can we apply SenCID to 10X Genomics sc-RNA seq?

LucasLiu20200131 commented 1 month ago

I have the same question about applying SenCID to 10X Genomics sc-RNA seq, looking forward to the reply.

SherryMiyano commented 3 weeks ago

Hello, thanks for the support for SenCID!

In the referenced description, I've included 10X Genomics into the generalized term of 'Dropseq' (in fact, Figure 2A, 2D and 2F are all from 10X), so feel free to perform SenCID on 10X Genomics. There's no difference in parameter settings between 10X, Dropseq or Smart-seq as input.

seasonzhao commented 3 weeks ago

Thank you so much! I will try it