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  • RNA-Seq on 2-cell co-culture system

    Hi all,

    our collaborators would like to perform an RNAseq experiment from a 2-cell co-culture system.

    For this experiment they would like to co-incubate fibroblasts and macrophages from 2 different backgrounds (Strains) of the same organism.

    After cultivating the cells, the bulk analysis should be able to separate both cell types. Either doing the analysis separately for each cell type, or doing it together, while being able to distinguish the two cell types.

    As this is also new to me, I was wondering, if anyone has heard of such analysis and whether or not this is feasible.

    Would it possible to have the RNA samples, that contain both RNA from fibroblasts and RNA from macrophages to sort the reads to the corresponding cell type and analyze them separately?

    The idea behind this kind of analysis is that the SNP should be different enough to be detected. One cell would have a SNP pattern from the first strain, while another one should have the SNP pattern of the second strain. They should have both different, but also overlapping transcriptome

    In other words, this method would only separate mRNAs (i) with a SNP(s), (ii) with a differential transcript pattern, and (iii) with information on cell-specific differences. Example: A macrophage-specific scavenger receptor from the first strain would not be expressed on the other cell in the pool and would have (in theory) a different SNP.

    Does anyone know of this kind of analysis? Any papers about it or any other sources?

    Thanks in advance

    Assa

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