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Marker genes of hematopoietic stem cells for cluster annotation in single-cell analysis

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
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updated by ATpoint ATpoint • written by Ribo • Ribo

Hi Ribo, I'm wondering if have get any progress in finding marker gene lists for these hematopoietic stem/progenitor cells? I'm now also in the stage of trying to find ways to annotate my single cell clusters from CD34+ enriched blood cells. I did try CellMarker2.0 and PanglaoDB, but seems like these datasets dont have much info about some of the very specific cell types.

Thanks in advance if you have any potential solutions to share!

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written by Yingying • Yingying

Hi Yingying,

Atlas of Blood Cells (ABC) portal is a single-cell database and web server for blood cells. In the 'Document' tab there are marker gene lists, but some cells are missing.

Another annotation approach is to compare the single-cell expression profiles with previously annotated reference datasets, and assign labels to each cluster based on the most similar reference cell. ABC portal contains many annotated single-cell transcriptomic datasets, so instead of using marker genes, you may try using one of these datasets as a reference to annotate your data.

If you come up with another solution, I'd love to hear about it :)

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written by Ribo • Ribo

Hi there. I am also doing a project in the following cell types: LT-HSC, ST-HSC, MPP, LMPP, GMP, MEP and CLP. Did you ever figure out a list of markers that can help?

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written by Ali • Ali

Read papers, scRNA-seq on HSPCs was done many times before, check how they annotated it. Research does not happen in a vacuum, you need tor read.

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written by ATpoint ATpoint

2 answers

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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written by Ribo • Ribo

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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written by ATpoint ATpoint

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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written by Ribo • Ribo

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