---
title: "Circadian gene expression in oligodendroglia"
author: "Luise A. Seeker"
date: "09/07/2021"
output: html_document
---
# Introduction
Erin Gibson gave an interesting talk about circardian genes and their effect
on oligodendroglia proliferation in depelopment and adverse effects of knocking
down one of the gey genes Bmal1 (Arntl) on cognitive and physical ability.
I wanted to test here if those genes are expressed in my dataset at all. It
may not be the ideal dataset to test this, because
1) I don't know at which time of the day the donors died
2) I don't see much evidenve for OPC proliferation
3) my samples are from adults which are beyond the highly dynamic stages of
childhood and adolescence
```{r}
library(Seurat)
library(here)
library(ggsci)
```
```{r, echo = F}
mypal <- pal_npg("nrc", alpha = 0.7)(10)
mypal2 <-pal_tron("legacy", alpha = 0.7)(7)
mypal3 <- pal_lancet("lanonc", alpha = 0.7)(9)
mypal4 <- pal_simpsons(palette = c("springfield"), alpha = 0.7)(16)
mypal5 <- pal_rickandmorty(palette = c("schwifty"), alpha = 0.7)(6)
mypal6 <- pal_futurama(palette = c("planetexpress"), alpha = 0.7)(5)
mypal7 <- pal_startrek(palette = c("uniform"), alpha = 0.7)(5)
mycoloursP<- c(mypal, mypal2, mypal3, mypal4, mypal5, mypal6, mypal7)
```
```{r}
nad_ol <- nad_ol <- readRDS(here("data",
"single_nuc_data",
"oligodendroglia",
"srt_oligos_and_opcs_LS.RDS"))
```
```{r}
seur_comb <- readRDS(here("data",
"single_nuc_data",
"all_cell_types",
"srt_anno_01.RDS"))
```
# Umap plots for orientiation
```{r}
DimPlot(seur_comb, cols = mycoloursP, label = TRUE) + NoLegend()
```
```{r}
DimPlot(nad_ol, cols = mycoloursP[6:40], label = TRUE) + NoLegend()
```
# Oligodendroglia
```{r}
FeaturePlot(nad_ol, features = "ARNTL")
```
```{r}
FeaturePlot(nad_ol, features = "ARNTL2")
```
```{r}
FeaturePlot(nad_ol, features = "BHLHE40")
```
```{r}
FeaturePlot(nad_ol, features = "BHLHE41")
```
```{r}
FeaturePlot(nad_ol, features = "CLOCK")
```
```{r}
FeaturePlot(nad_ol, features = "CSNK1E")
```
```{r}
FeaturePlot(nad_ol, features = "CRY1")
```
```{r}
FeaturePlot(nad_ol, features = "CRY2")
```
```{r}
FeaturePlot(nad_ol, features = "NR1D1")
```
```{r}
FeaturePlot(nad_ol, features = "NR1D2")
```
```{r}
#FeaturePlot(nad_ol, features = "PER1") # Not expressed, not in dataset
```
```{r}
FeaturePlot(nad_ol, features = "PER2")
```
```{r}
FeaturePlot(nad_ol, features = "PER3")
```
```{r}
FeaturePlot(nad_ol, features = "RORA")
```
# Whole dataset
```{r}
FeaturePlot(seur_comb, features = "ARNTL")
```
```{r}
FeaturePlot(seur_comb, features = "ARNTL2")
```
```{r}
FeaturePlot(seur_comb, features = "BHLHE40")
```
```{r}
FeaturePlot(seur_comb, features = "BHLHE41")
```
```{r}
FeaturePlot(seur_comb, features = "CLOCK")
```
```{r}
FeaturePlot(seur_comb, features = "CSNK1E")
```
```{r}
FeaturePlot(seur_comb, features = "CRY1")
```
```{r}
FeaturePlot(seur_comb, features = "CRY2")
```
```{r}
FeaturePlot(seur_comb, features = "NR1D1")
```
```{r}
FeaturePlot(seur_comb, features = "NR1D2")
```
```{r}
#FeaturePlot(seur_comb, features = "PER1") # Not expressed, not in dataset
```
```{r}
FeaturePlot(seur_comb, features = "PER2")
```
```{r}
FeaturePlot(seur_comb, features = "PER3")
```
```{r}
FeaturePlot(seur_comb, features = "RORA")
```
# Session Info
```{r}
sessionInfo()
```