human adult updates

linnarsson-lab · Sep 19, 2019 · 7d9f7e1 · 7d9f7e1
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diff --git a/Human_adult/Ectoderm/ASTRO.md b/Human_adult/Ectoderm/ASTRO.md
@@ -4,7 +4,7 @@ definition: +AQP4 +GJA1 +GLI3 +LAMA1
 go:
 shogoin: 
 uberon:
-categories: Ectodermal Neuroectodermal
+categories: Ectodermal Neuroectodermal Glial
 version: 1
 synonyms:
 ---

diff --git a/Human_adult/Ectoderm/BERG.md b/Human_adult/Ectoderm/BERG.md
@@ -4,7 +4,7 @@ definition: +AQP4 +GDF10 +GABRG3 +WIF1 +LGR6
 go:
 shogoin: 
 uberon:
-categories: Ectodermal Neuroectodermal
+categories: Ectodermal Neuroectodermal Glial
 version: 1
 synonyms:
 ---

diff --git a/Human_adult/Ectoderm/E-SCHWL.md b/Human_adult/Ectoderm/E-SCHWL.md
@@ -1,7 +1,7 @@
 name: Schwann cell-like
 abbreviation: E-SCHWL
 definition: +MPZ
-categories: Ectodermal Neuroectodermal
+categories: Ectodermal Neuroectodermal Glial
 ---
 
 Expressing the Schwann marker MPZ
diff --git a/Human_adult/Ectoderm/NBL.md b/Human_adult/Ectoderm/NBL.md
@@ -4,7 +4,7 @@ definition: +NHLH1
 go:
 shogoin: 
 uberon:
-categories: Ectodermal Neuronal Neuroectodermal
+categories: Ectodermal Neuroectodermal Neuronal
 version: 1
 synonyms:
 ---

diff --git a/Human_adult/Ectoderm/NEUR.md b/Human_adult/Ectoderm/NEUR.md
@@ -4,7 +4,7 @@ definition: +RBFOX3
 go:
 shogoin: 
 uberon:
-categories: Ectodermal Neuronal Neuroectodermal
+categories: Ectodermal Neuroectodermal Neuronal
 version: 1
 synonyms:
 ---

diff --git a/Human_adult/Ectoderm/OLIGO.md b/Human_adult/Ectoderm/OLIGO.md
@@ -4,7 +4,7 @@ definition: +PLP1 +MBP +MOG -PDGFRA
 go:
 shogoin: 
 uberon:
-categories: Ectodermal Neuroectodermal
+categories: Ectodermal Neuroectodermal Glial
 version: 1
 synonyms:
 ---
diff --git a/Human_adult/Ectoderm/OPC.md b/Human_adult/Ectoderm/OPC.md
@@ -4,7 +4,7 @@ definition: +SOX10 +PDGFRA
 go:
 shogoin: 
 uberon:
-categories: Ectodermal Neuroectodermal
+categories: Ectodermal Neuroectodermal Glial
 version: 1
 synonyms:
 ---
diff --git a/Human_adult/Ectoderm/RGL.md b/Human_adult/Ectoderm/RGL.md
@@ -1,7 +1,7 @@
 name: Radial glia
 abbreviation: RGL
 definition: +FABP7 +VIM +NES +SOX2 +HES1
-categories: Ectodermal Neuroectodermal
+categories: Ectodermal Neuroectodermal Glial
 ---
 
 Radial glia across the whole neural tube
diff --git a/Human_adult/Ectoderm/UBC.md b/Human_adult/Ectoderm/UBC.md
@@ -0,0 +1,12 @@
+name: Unipolar brush cell
+abbreviation: UBC
+definition: +GRIA2 +EOMES
+go:
+shogoin: 
+uberon: 
+categories: Ectodermal Neuroectodermal Neuronal
+version: 1
+synonyms:
+---
+
+https://www.jneurosci.org/content/26/36/9184
diff --git a/Human_adult/Mesoderm/M-BCELL.md b/Human_adult/Mesoderm/M-BCELL.md
@@ -0,0 +1,15 @@
+name: B cells
+abbreviation: M-BCELL.md
+definition: +DOCK8 +PAX5 +FCRL1
+go:
+shogoin: 
+uberon:
+categories: Endomesodermal
+version: 1
+synonyms:
+---
+
+PAX5: https://www.sciencedirect.com/science/article/pii/S1074761307003317
+FCRL1: 
+    http://www.bloodjournal.org/content/105/3/1121?sso-checked=true
+    https://www.jimmunol.org/content/196/10/4064
diff --git a/Human_adult/Mesoderm/M-ENDO.md b/Human_adult/Mesoderm/M-ENDO.md
@@ -1,6 +1,6 @@
 name: Endothelial (mesoderm)
 abbreviation: M-ENDO
-definition: +CLDN5 +FLT1 +CD34 
+definition: +CLDN5 +FLT1
 go:
 shogoin: 
 uberon:
@@ -9,3 +9,5 @@ version: 1
 synonyms:
 ---
 
+Removed CD34 because it excluded a KCNJ6+ population likely to be endothelial
+FLT1 also labels microglia, but CLDN5 does not.
diff --git a/Human_adult/Mesoderm/M-MGL.md b/Human_adult/Mesoderm/M-MGL.md
@@ -1,6 +1,6 @@
 name: Microglia (mesoderm) 
 abbreviation: M-MGL 
-definition: +TYROBP +DOCK8
+definition: +TYROBP +DOCK8 -CD163 -GZMB
 go: 
 shogoin: 
 uberon: 
@@ -9,4 +9,9 @@ version: 1
 synonyms:
 ---
 
-Markers from adult human data
+CD163, TMEM119: Tasic et. al., 2019 (mouse) and 
+Tmem119: 
+    Bottcher et al., 2019 (human, mass cytometry)
+    Tmem119 is specific but not highly enough expressed to use as a marker
+
+Adding GZMB to avoid labeling NK cells.
diff --git a/Human_adult/Mesoderm/M-NK.md b/Human_adult/Mesoderm/M-NK.md
@@ -0,0 +1,13 @@
+name: NK cells
+abbreviation: M-NK.md
+definition: +NCAM1 +GZMB
+go:
+shogoin: 
+uberon:
+categories: Endomesodermal
+version: 1
+synonyms:
+---
+
+NCAM1: Bottcher et al. 2019
+Adult human data + wikipedia pages for GZMB, natural killer cells
diff --git a/Human_adult/Mesoderm/M-PER.md b/Human_adult/Mesoderm/M-PER.md
@@ -1,6 +1,6 @@
 name: Pericytes (mesoderm)
 abbreviation: M-PER
-definition: +TAGLN
+definition: +PDGFRB +ENSG00000143248 -MYH11
 go:
 shogoin: 
 uberon:
@@ -9,3 +9,11 @@ version: 1
 synonyms:
 ---
 
+RGS5: https://doi.org/10.1096/fj.02-0340fje
+
+PDGFRB, ANPEP (in a subset): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745011/
+
+MYH11, MYOCD, CNN1, NG2 / CSPG4: 
+    https://www.cell.com/cell-reports/pdf/S2211-1247(17)30644-7.pdf
+    https://anatomypubs.onlinelibrary.wiley.com/doi/full/10.1002/dvdy.1200
+    "For example, the absence of α‐smooth muscle actin (SMA) on NG2‐positive cells in CNS capillaries has led some workers to the erroneous conclusion that NG2 is expressed by endothelial cells, rather than mural cells, in this microvasculature (Schrappe et al., 1991; Grako and Stallcup, 1995). Our current results demonstrate that, although SMA is an excellent marker for smooth muscle cells, it is not always an appropriate marker for pericytes in vivo."
diff --git a/Human_adult/Mesoderm/M-PER2.md b/Human_adult/Mesoderm/M-PER2.md
diff --git a/Human_adult/Mesoderm/M-PVM.md b/Human_adult/Mesoderm/M-PVM.md
@@ -1,12 +1,12 @@
 name: Perivascular macrophage (mesoderm)
 abbreviation: M-PVM
-definition: +AIF1 +MRC1 -TMEM119
+definition: +AIF1 +MRC1 +CD163
 go:
 shogoin: 
 uberon:
 categories: Endomesodermal
 version: 1
 synonyms:
 ---
-
-In adult human data, one cluster is MRC1+ and TMEM119+ (should be specific for PVM, microglia respectively). Probably microglia based on other markers (e.g. CTSS, P2RY12)
+CD163, TMEM119: Tasic et. al., 2019 (mouse) and 
+Tmem119: Bottcher et al., 2019 (human, mass cytometry)
diff --git a/Human_adult/Mesoderm/M-TCELL.md b/Human_adult/Mesoderm/M-TCELL.md
@@ -0,0 +1,13 @@
+name: T cells
+abbreviation: M-TCELL
+definition: +DOCK8 +CD8A +CD3G
+go:
+shogoin: 
+uberon:
+categories: Endomesodermal
+version: 1
+synonyms:
+---
+DOCK8: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201196/
+CD8: https://www.nature.com/articles/s41467-018-07053-9
+CD3: Bottcher et al 2019
diff --git a/Human_adult/Mesoderm/M-VSMC.md b/Human_adult/Mesoderm/M-VSMC.md
@@ -0,0 +1,17 @@
+name: Vascular smooth muscle cell
+abbreviation: M-VSMC
+definition: +PDGFRB +ACTA2 +MYH11
+go:
+shogoin: 
+uberon:
+categories: Endomesodermal
+version: 1
+synonyms:
+---
+
+RGS5: https://doi.org/10.1096/fj.02-0340fje
+PDGFRB: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745011/
+MYH11, MYOCD, CNN1, NG2 / CSPG4: 
+    https://www.cell.com/cell-reports/pdf/S2211-1247(17)30644-7.pdf
+    https://anatomypubs.onlinelibrary.wiley.com/doi/full/10.1002/dvdy.1200
+    "For example, the absence of α‐smooth muscle actin (SMA) on NG2‐positive cells in CNS capillaries has led some workers to the erroneous conclusion that NG2 is expressed by endothelial cells, rather than mural cells, in this microvasculature (Schrappe et al., 1991; Grako and Stallcup, 1995). Our current results demonstrate that, although SMA is an excellent marker for smooth muscle cells, it is not always an appropriate marker for pericytes in vivo."