Eccentric medium spiny neuron (eMSN)

[ME/CFS Science Blog]

Here is a dropbox link with:

• Data underlying the HBA MAGMA plot for DecodeME
• Supplementary material from the Duncan et al. paper "Mapping the cellular etiology of schizophrenia and complex brain phenotypes" which I used to annotate the cell types in the plot.

Wow, thanks. Much appreciated! I noticed that cluster 133 (the yellow dot just below the significance threshold) is also upper-layer intratelencephalic neurons located in the cortex.

I do wonder what distinguishes cluster 136 and 133 of IT cells from other ITs that don't come near the significance threshold.

 

[ME/CFS Science Blog]

I do wonder what distinguishes cluster 136 and 133 of IT cells from other ITs that don't come near the significance threshold.

Cluster 136, mostly in the amygdala has only 152 cells compared to, for example 20.000 for cluster 133, so perhaps that makes it less reliable and more likely to be a fluke?

Cluster 133 has the following dissections:

V1C:62.92%, V2:17.60%, Pro:14.65%, M1C:2.37%, A1C:1.23%, Ig:0.32%, A29-A30:0.28%, STG:0.20%, S1C:0.17%, A5-A7:0.07%, TF:0.04%, A23:0.03%, A19:0.02%, MTG:0.01%, A13:0.01%, Cla:0.01%, A32:0.00%, A44-A45:0.00%, MEC:0.00%, MN:0.00%, A40:0.00%, TH-TL:0.00%, A43:0.00%, LG:0.00%,

The labels are explained here:
Human Brain Cell Atlas v1.0 - Overview - HCA Data Portal

V1C = Primary Visual Cortex
V2 = Peristriate Cortex
Pro = Area Prostriata

So 95% was taken from the visual cortex and related areas.

 

[ME/CFS Science Blog]

PCDH17
PCDH17 Gene - GeneCards | PCD17 Protein | PCD17 Antibody
A bit speculative this one because the hit (13:58,456,743 T/C) only reached the 10^-6 threshold in DecodeME, and the gene is quite far off.

But PCDH17 "plays a pivotal role in synaptic development and neural circuit refinement. It is enriched at corticobasal ganglia synapses where it regulates presynaptic assembly, and its deficiency results in altered vesicle accumulation and synaptic transmission efficiency."

(To clarify: this is likely part of the same signal that points to eMSN, so a different way of looking at the same thing, not extra confirmation of it)