in vitro primary microglia
Data analysis of in vitro microglia secretion of IL-6 and TNFa protein into the cell culture supernatant in response to a 12 hour LPS and IFNg treatment. For each independent culture experiment the control was set to one and log normalized.
Samples
## , , = Ctx
##
##
## E18 Adult
## CON 5 4
## MIA 5 4
##
## , , = Str
##
##
## E18 Adult
## CON 4 4
## MIA 4 4data2 <- pivot_longer(data, cols = starts_with("Log2"), names_to = "cytokine", values_to = "log2FC")
data2 %>% filter(Group=="MIA" & Region=="Ctx") %>% ggplot(., aes(x=Age, y=log2FC, color = cytokine, group = cytokine)) + geom_point(aes(group = cytokine), position = position_jitterdodge(dodge.width=0.7, jitter.width = 0.15), size = 3) + geom_hline(yintercept = 0) + stat_summary(fun.data=mean_se, color="black", shape = 3, size=1, position = position_dodge(width = 0.5)) + ylim(-1.3, 1.3) + labs(y="FC (log2)") + theme(legend.position ="none") + labs(subtitle = "cortex") + theme_cowplot() + scale_color_manual(values = c("red", "red4"))
data2 %>% filter(Group=="MIA" & Region=="Str") %>% ggplot(., aes(x=Age, y=log2FC, color = cytokine, group = cytokine)) + geom_point(aes(group = cytokine), position = position_jitterdodge(dodge.width=0.7, jitter.width = 0.15), size = 3) + geom_hline(yintercept = 0) + stat_summary(fun.data=mean_se, color="black", shape = 3, size=1, position = position_dodge(width = 0.5)) + ylim(-1.3, 1.3) + labs(y="FC (log2)") + theme(legend.position ="none") + labs(subtitle = "striatum") + theme_cowplot() + scale_color_manual(values = c("red", "red4"))
# Effect of Sex
data2 %>% filter(Group=="MIA" & Region=="Ctx") %>% ggplot(., aes(x=Age, y=log2FC, color = Sex, group = cytokine)) + geom_point(aes(group = cytokine), position = position_jitterdodge(dodge.width=0.7, jitter.width = 0.15), size = 3) + geom_hline(yintercept = 0) + stat_summary(fun.data=mean_se, color="black", shape = 3, size=1, position = position_dodge(width = 0.5)) + ylim(-1.3, 1.3) + labs(y="FC (log2)") + theme(legend.position ="none") + labs(subtitle = "Ctx") + theme_cowplot() + scale_color_manual(values = c("deeppink2", "blue"))
data2 %>% filter(Group=="MIA" & Region=="Str") %>% ggplot(., aes(x=Age, y=log2FC, color = Sex, group = cytokine)) + geom_point(aes(group = cytokine), position = position_jitterdodge(dodge.width=0.7, jitter.width = 0.15), size = 3) + geom_hline(yintercept = 0) + stat_summary(fun.data=mean_se, color="black", shape = 3, size=1, position = position_dodge(width = 0.5)) + ylim(-1.3, 1.3) + labs(y="FC (log2)") + theme(legend.position ="none") + labs(subtitle = "Ctx") + theme_cowplot() + scale_color_manual(values = c("deeppink2", "blue"))
Shapiro-Wilk test for normality
## # A tibble: 4 x 5
## Age Region variable statistic p
## <fct> <chr> <chr> <dbl> <dbl>
## 1 E18 Ctx Log2IL6 0.993 0.990
## 2 E18 Str Log2IL6 0.911 0.486
## 3 Adult Ctx Log2IL6 0.993 0.974
## 4 Adult Str Log2IL6 0.902 0.443## # A tibble: 4 x 5
## Age Region variable statistic p
## <fct> <chr> <chr> <dbl> <dbl>
## 1 E18 Ctx Log2TNFa 0.971 0.881
## 2 E18 Str Log2TNFa 0.907 0.468
## 3 Adult Ctx Log2TNFa 0.877 0.328
## 4 Adult Str Log2TNFa 0.862 0.269Perform one-sample t-test
## IL-6## Adding missing grouping variables: `Region`, `Age`## # A tibble: 17 x 6
## # Groups: Region, Age [4]
## Region Age Log2IL6 pval stat df
## <chr> <fct> <dbl> <dbl> <dbl> <dbl>
## 1 Ctx Adult -0.434 0.0603 -2.94 3
## 2 Ctx Adult -0.599 0.0603 -2.94 3
## 3 Ctx Adult -0.269 0.0603 -2.94 3
## 4 Ctx Adult -0.0589 0.0603 -2.94 3
## 5 Ctx E18 -0.621 0.401 0.939 4
## 6 Ctx E18 0.651 0.401 0.939 4
## 7 Ctx E18 0 0.401 0.939 4
## 8 Ctx E18 1.07 0.401 0.939 4
## 9 Ctx E18 0.251 0.401 0.939 4
## 10 Str Adult -0.737 0.0463 -3.28 3
## 11 Str Adult -0.269 0.0463 -3.28 3
## 12 Str Adult -0.168 0.0463 -3.28 3
## 13 Str Adult -0.621 0.0463 -3.28 3
## 14 Str E18 -0.454 0.00396 -8.08 3
## 15 Str E18 -0.786 0.00396 -8.08 3
## 16 Str E18 -0.578 0.00396 -8.08 3
## 17 Str E18 -0.515 0.00396 -8.08 3## TNFa
## Adding missing grouping variables: `Region`, `Age`## # A tibble: 17 x 6
## # Groups: Region, Age [4]
## Region Age Log2TNFa pval stat df
## <chr> <fct> <dbl> <dbl> <dbl> <dbl>
## 1 Ctx Adult 0.310 0.352 -1.10 3
## 2 Ctx Adult -0.578 0.352 -1.10 3
## 3 Ctx Adult -0.0893 0.352 -1.10 3
## 4 Ctx Adult -0.599 0.352 -1.10 3
## 5 Ctx E18 -1.15 0.765 0.320 4
## 6 Ctx E18 -0.218 0.765 0.320 4
## 7 Ctx E18 0.345 0.765 0.320 4
## 8 Ctx E18 1.28 0.765 0.320 4
## 9 Ctx E18 0.390 0.765 0.320 4
## 10 Str Adult -0.621 0.0478 -3.24 3
## 11 Str Adult -0.252 0.0478 -3.24 3
## 12 Str Adult -0.252 0.0478 -3.24 3
## 13 Str Adult -0.889 0.0478 -3.24 3
## 14 Str E18 -0.713 0.0316 -3.82 3
## 15 Str E18 -0.474 0.0316 -3.82 3
## 16 Str E18 -0.136 0.0316 -3.82 3
## 17 Str E18 -0.644 0.0316 -3.82 3Conclusion: Striatum microglia showed significantly less IL-6 and TNFa secretion at both E18 and Adult. Cortex microglia do not show a change in secretion at E18, and a mild IL-6 reduction in adult.
Reproducibility info
## [1] "2021-11-02 12:17:42 EDT"## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.0.3 (2020-10-10)
## os macOS Big Sur 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2021-11-02
##
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## [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library