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Help mapping cell types to correct CL ontologies #73

Closed pnejad closed 3 years ago

pnejad commented 3 years ago

We are wrangling GSE89322 and need to map their cell types to CL ontologies. Could you please help us map to the correct ontology?

classic dendritic cell (cDCs)

precursor dendritic cell (pre-DCs)

Here is a description from their paper(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599345/): For sorting pre-cDCs, enriched cells were stained for CD14 (TuK4, Qdot-655, Invitrogen), CD3 (OKT3, Brilliant Violet (BV) 650, Biolegend), CD19 (HIB19, BV650, Biolegend), CD56 (HCD56, BV650, Biolegend), CD66b (G10F5, PerCP-Cy5.5, Biolegend), CD303 (201A, PerCP-Cy5.5, Biolegend), CD1c (L161, APC-Cy7, Biolegend), CD141 (M80, PE-Cy7, Biolegend), CD34 (581, AlexaFluor700, Biolegend), CD117 (104D2, BV421, Biolegend), CD135 (4G8, PE, BD), CD45RA (HI100, BV510, Biolegend), CD116 (4H1, FITC, Biolegend) and CD115 (9-4D2-1E4, APC, Biolegend) for 40 min on ice. Pre-cDCs were isolated as Lin(CD3/19/56/14)- Granulocyte(CD66b)-pDC(CD303)-cDC(CD1c/CD141)-CD34-CD117 + CD135 + SSC lo CD116 + CD115-CD45RA+ cells. cDC1 were isolated as Lin(CD3/19/56/14)- Granulocyte(CD66b)-pDC(CD303)-CD141+ cells. cDC2 were isolated as Lin(CD3/19/56/14)- Granulocyte(CD66b)-pDC(CD303)-CD1c + cells.

paolaroncaglia commented 3 years ago

Hi @pnejad ,

conventional dendritic cell (CL:0000990) is defined as “Conventional dendritic cell is a dendritic cell that is CD11c-high.”. Does this fit with the paper? Also from this other paper PMID: 23516985, if it helps: “Classical Dendritic Cells cDCs refer to all DCs other than pDCs [Plasmacytoid Dendritic Cells]. cDCs form a small subset of tissue hematopoietic cells that populate most lymphoid and nonlymphoid tissues.”

If conventional dendritic cell (CL:0000990) is appropriate to use, then pre-conventional dendritic cell (CL:0002010) would be appropriate to represent precursor dendritic cell (pre-DCs).

You may also consider the human-specific CL:0001056 'dendritic cell, human' (definition "A dendritic cell with the phenotype HLA-DRA-positive.”, rdfs:comment "This cell type is compatible with the HIPC Lyoplate markers for 'dendritic cell'. The inclusion of HLA-DRA in the definition restricts this definition to human dendritic cells.”)

Let me know if you have any concern and I might consult with one of the CL experts.

pnejad commented 3 years ago

@paolaroncaglia Thank you for your feedback! I think I will use conventional dendritic for this dataset. The paper refers to conventional and classical dendritic cells as cDC's, which makes me believe they are the same.

paolaroncaglia commented 3 years ago

@pnejad Thanks. I'll close this ticket then.