Marker genes of hematopoietic stem cells for cluster annotation in single-cell analysis
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8 weeks ago
Ribo ▴ 20

Hi,

I perform a single-cell analysis of mouse hematopoietic stem cells. I'd like to reveal the cell types within the dataset based on cluster-specific expression of marker genes, so I'm looking for a marker gene list of hematopoietic stem and progenitor cells.

More specifically, I'd like to identify the following cell types: LT-HSC, ST-HSC, MPP, LMPP, GMP, MEP and CLP.

Does anybody know where I can find such list for cluster annotation?

Thanks in advance.

single-cell cluster-annotation hsc marker-gene • 447 views
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6 weeks ago
Ribo ▴ 20

CellMarker is a manually curated resource used for browsing, searching and downloading markers of diverse cell types of different tissues in human and mouse.

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8 weeks ago
ATpoint 66k

HSPC is a broad and heterogeneous group of cells. See work from the Ido Amit lab for example Paul et al and Giladi et al, in which many markers are being discussed. See also https://www.nature.com/articles/s41586-022-04571-x which defined scorecards for the HSC itself. Usually it comes down to a good literature search. Domain knowledge is key, and the hematopoietic system is arguably one of the most intensly research compartment of the organism, so there is a large stack of literature available. It all depends on the resolution you want to annotate with and which types of cells you have to distinguish your population from.

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Thanks for your comment! I have in fact read these papers, but they mostly discuss marker genes of mature cells (monocyte, erythrocyte, etc.), while I'm interested in stem and progenitor cells. I edited my question now to be more specific.

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