Help in joint analysis of laser capture RNA-Seq with scRNA-Seq

Help in joint analysis of laser capture RNA-Seq with scRNA-Seq

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I have RNA seq data that I captured using laser capture. the data is from a single cell layer of tissue from embryonic origin. I collected 16 samples from different locations of this layer from 4 different embryos (total 64 samples). I want to use published single-cell RNA-Seq data of the same tissue from different time points during development together with my data to perform analysis that will show that my different spatial locations are in different differentiation states (maybe pseudo time analysis and trajectory??).

I will really appreciate it if someone has an idea of how to approach this problem?

Thank you very much!


RNA

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