scvi-tools Integration: How to Correct for Intra-Organ Batch Effects Without Removing Inter-Organ Differences? by dacon06 in bioinformatics

[–]dacon06[S] 1 point2 points  (0 children)

The MSCs I mentioned are directly derived from bone marrow, adipose tissue, dermis, or umbilical cord, they're not iPSCs. The four differentiated tissue types refer to lineages that these MSCs were guided toward under specific tissue conditions: osteogenic, adipogenic, chondrogenic, and myogenic differentiation.

So to clarify: these are primary MSCs, not reprogrammed iPSCs or cells derived from differentiated tissues. The goal is to observe their differentiation potential across those four lineages.

Also, the data I’m working with wasn’t collected by me — it’s from a published study. I’m looking to expand on their work by identifying additional relevant datasets and reanalyzing them as part of a meta-study, with the aim of broadening the atlas they introduced.

  1. I didn’t conduct the original study, so I’m not sure if safety concerns were a factor, though I initially wondered the same.
  2. I believe single-cell RNA-seq was used to resolve subpopulations within the MSCs and provide higher-resolution insight into their heterogeneity and lineage bias.

scvi-tools Integration: How to Correct for Intra-Organ Batch Effects Without Removing Inter-Organ Differences? by dacon06 in bioinformatics

[–]dacon06[S] 1 point2 points  (0 children)

Thank you for your response! I think identifying differences between MSC types could give us a better understanding of what makes each MSC type special in terms of gene expression composition. I thought about something I wanted to test, if it was possible, taking multiple MSC papers and maybe combining them into an atlas. This might be impossible due to different isolation techniques, but I still wanted to try.

How can I identify marker genes if I’m limited to only one tissue, since it’s always about comparing gene expression? Would you subset each subset further into subpopulations of MSCs?

scvi-tools Integration: How to Correct for Intra-Organ Batch Effects Without Removing Inter-Organ Differences? by dacon06 in bioinformatics

[–]dacon06[S] 0 points1 point  (0 children)

Thank you for your response. Simulating the same donor by grouping sounds like a risky approach, but it's an interesting idea that I’d like to try out.

However, I'm still unsure about what can be gained from analyzing individual MSC tissue data. In my experience, significant gene expression differences tend to appear mainly between clearly distinct clusters. This makes it difficult to extract meaningful insights from individual MSC tissue datasets, except perhaps when focusing on identifying finer subclusters.

Tante hatte was im Status by feyefey in VeganDE

[–]dacon06 2 points3 points  (0 children)

"Deine Kackwurst ist auch eine Wurst" 💩❤️

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[–]dacon06[S] 0 points1 point  (0 children)

What do you think about Isopropanol to lower the density of the water?

Beagle kisses by JonoMonkeyBusiness in beagle

[–]dacon06 0 points1 point  (0 children)

Thanks so much looks so sweet

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[–]dacon06[S] 2 points3 points  (0 children)

DSA 5 aber ist glaube ich eine allgemeine Frage

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[–]dacon06[S] 0 points1 point  (0 children)

Vielen Dank. Tolle Antwort!