Looking for dataset with scRNA-seq data for normal (non cancer, non iPSCs) but prolifirating cells human (may be mouse or other )
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5 weeks ago
Alexander ▴ 20

I am looking for srRNAseq dataset for the purpose of the cell cycle analysis. We have already looked on many cancer cell lines data, but want to check certain things on "normal cells". The problem is that normal cells are not much prolifirating. But still there is some prolifiration for some types of cells - I would be happy for recomendation for any kind of such dataset (and publication). Preferably for human cells, but other suggestions are also welcome.

Preferably the cells should not be differentiating - otherwise it would be a problem to distinguish the cell cycle trajectory from differentiation one.

[EDIT:] It seems fibroblasts - what we need. But are there any other examples ? And are the single cell data for fibroblasts ? Cell cycle for fibroblasts was analysed in Tom Freeman's papers e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6788831/ but that seems not a single cell data , but synchronized cell populations.

PS

S. Nestorova dataset used in scanpy and seurat tutorials is not good for that reason - the main story is about differentiation and cell cycle analysis seems to suffer from that.

PSPS

RNA-seq • 335 views
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So you want proliferating but non-differentiating cells, is that correct?

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Yes, exactly ! And preferably not stem cells (or iPCS). And also ideally cells of just one type (cells of different types may have different details of cell cycle (we see that on cancer cell lines). Well, any comment is welcome.

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It seems fibroblasts might be one example , but may be some other cells ? (Made edit to question).

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5 weeks ago

Lots of options in the scRNAseq package, though I don't know which might be most appropriate for your purpose.

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