Results
DV genes
"HVGs and LVGs were determined using BASiCs (data as described in Vallejos et al., 2015). Estimated read counts from Salmon (rounded to integer values) were used as input. HVGs were detected at a variance contribution threshold of 89% leading to an optimized evidence threshold of 0.5145 and giving an estimated false discovery rate of 5.71% and an estimated false negative rate of 5.7%. LVGs were detected at a variance contribution threshold of 40% with an optimized evidence threshold of 0.8115 and estimated false discovery rate and estimated false negative rate both of 2.28%. The value sigma indicates the proportion of the total variability that is due to biological heterogeneity."
MHC genes scRNA-seq
" We analyzed the expression of 14 genes involved in the MHC type I pathway, major histocompatibility complex, class I, A (
HLA-A), B (
HLA-B), and C (
HLA-C); beta-2-microglobulin (
B2M); as well as tapasin (
TAPBP); calreticulin (
CALR); endoplasmic reticulum aminopeptidase 1 (
ERAP1); heat shock 70 kDa protein 5 (
HSPA5); protein disulfide isomerase family A, member 3 (
PDIA3); transporter 2, ATP-binding cassette, sub-family B (
TAP2); and the members of the
SEC61 complex (
SEC61A1,
SEC61A2,
SEC61B, and
SEC61G), in neuronal cells of the adult brain as well as pre- and postmitotic neuronal progenitors from prenatal brain. We also included endothelial cells and microglia as positive controls for MHCI expression (
Fig. 5). Our results show that MHCI genes are clearly expressed in a subset of neurons in the adult brain.
Neurons do not express MHCI genes highly at a population level, but there is a significant subset of neurons that express the genes to the same level as endothelial cells and microglia.
We also found that neurons expressing MHC-related genes do so in a coordinated fashion with most neurons expressing between six and eight of the investigated genes at the same time (
SI Appendix, Figs. S10 and S11). Our results suggest that a subset of adult brain neurons are not immunologically inert, and demonstrate the power of single cell measurements given that the expression of these genes would likely be undetected at a population level. "
"The highly variable subset included genes with low expression levels, where biological variability is less readily discernible from the technical noise. However, it also included genes with transcription levels that likely represent functional heterogeneity such as the secretory leukocyte protease inhibitor Slpi and the chemokine receptor Ccr7." "Essentially, each B cell has a unique complement of expressed V genes because of the rearrangement of its antigen receptor. Single-cell transcriptomes revealed the biological heterogeneity exemplified by the IgV genes, which were among the highly variable transcripts identified by the BASiCs algorithm (Fig. 3 C). Even highly synchronous and developmentally equivalent B cells showed a high degree of heterogeneity in the expression of master regulator genes, notably transcription factors, which were enriched in the HVG subset (Fig. 3 C and Table S4)."
Power analysis
Data sources:
CNS scRNA-seq data
"Human hippocampus and PFC samples. -- Human hippocampus and PFC samples were obtained from the Genotype-Tissue Expression (GTEx) project. Samples were originally collected from recently deceased, non-diseased donors
18,
23. For this study, we selected samples of frozen hippocampus and PFC from five male donors, aged 40–65 (including three samples of PFC and four samples of hippocampus). "
Liver scRNA-seq data
vQTL related references;
‘Particle genetics’: treating every cell as unique
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
Weight, Age and Coefficients of Variation in Renal Solute Excretion
Sex modifies genetic effects on residual variance in urinary calcium excretion in rat (Rattus norvegicus).