Merge pull request #255 from lilab-bcb/boli

Added Germinal Center B cell markers
lilab-bcb · Dec 4, 2022 · cb1f4d4 · cb1f4d4
2 parents 62dd3dd + 2dcf506
commit cb1f4d4
Showing 1 changed file with 49 additions and 3 deletions.
diff --git a/pegasus/annotate_cluster/human_immune_cell_markers.json b/pegasus/annotate_cluster/human_immune_cell_markers.json
@@ -123,9 +123,9 @@
 						"name" : "Naive B cell",
 						"markers" : [
 							{
-								"genes" : ["TCL1A+", "FCER2+"],
+								"genes" : ["IGHD+", "TCL1A+", "FCER2+"],
 								"weight" : 1.0,
-								"comments" : "markers for naive B cell, collected from Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper. Validated using ICA pbmc data."
+								"comments" : "markers for naive B cell, collected from Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper. Validated using ICA pbmc data"
 							}
 						]
 					},
@@ -135,7 +135,53 @@
 							{
 								"genes" : ["CD27+", "TNFRSF13B+"],
 								"weight" : 1.0,
-								"comments" : "markers for memory B cell, collected from Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper. Validated using ICA pbmc data."
+								"comments" : "markers for memory B cell, collected from Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper. Validated using ICA pbmc data"
+							}
+						]
+					}
+				]
+			}
+		},
+
+		{
+			"name" : "Germinal Center B cell",
+			"markers" : [
+				{
+					"genes" : ["CD19+", "MS4A1+", "CD79A+", "CD79B+"],
+					"weight" : 0.3,
+					"comment" : "CD19, CD20 and CD79"
+				},
+				{
+					"genes" : ["CD38+", "BCL6+", "BCL2-", "RGS13+"],
+					"weight" : 0.6,
+					"comment" : "First 3 markers are from Klein et al. PNAS 2003 https://doi.org/10.1073/pnas.0437996100 (Fig. 1 & 2). The last marker is from XXX"
+				},
+				{
+					"genes" : ["PCNA+", "MKI67+"],
+					"weight" : 0.1,
+					"comment" : "From Klein et al. PNAS 2003 https://doi.org/10.1073/pnas.0437996100 (Fig. 2)"
+				}
+			],
+			"subtypes" : {
+				"title" : "GC B cell subtype markers",
+				"cell_types" : [
+					{
+						"name" : "Dark zone B cell",
+						"markers" : [
+							{
+								"genes" : ["CXCR4+", "AICDA+", "FOXP1+", "MME+"],
+								"weight" : 1.0,
+								"comment" : "Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper"
+							}
+						]
+					},
+					{
+						"name" : "Light zone B cell",
+						"markers" : [
+							{
+								"genes" : ["CD83+", "LMO2+"],
+								"weight" : 1.0,
+								"comment" : "Fig. 4B of Massoni-Badosa et al. Tonsil Atlas paper"
 							}
 						]
 					}