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Last updated: 2020-04-02
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Knit directory: 20170327_Psen2S4Ter_RNASeq/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | bad81c1 | Steve Ped | 2020-03-05 | Updated MutVsWt UpSet plots for KEGG/HALLMARK |
| Rmd | f75f82a | Steve Ped | 2020-03-04 | Added post-CQN PCA |
| html | 86ffa07 | Steve Ped | 2020-02-20 | Updated saample layout figure |
| Rmd | 4d2af23 | Steve Ped | 2020-02-19 | Modified heatmap sizes & initial network layout |
| html | 876e40f | Steve Ped | 2020-02-17 | Compiled after minor corrections |
| html | 1032a6d | Steve Ped | 2020-01-28 | Added link to HomVsHet |
| Rmd | 9104ecd | Steve Ped | 2020-01-28 | First draft of Hom Vs Het |
| html | 468e6e3 | Steve Ped | 2020-01-28 | Ran enrichment of Mut Vs WT |
| Rmd | 3a9933c | Steve Ped | 2020-01-28 | Finished Enrichment analysis on MutVsWt |
| html | b086aff | Steve Ped | 2020-01-26 | Added first step of enrichment analysis |
| Rmd | ba189be | Steve Ped | 2020-01-26 | Corrected packages |
| html | 96d8cc7 | Steve Ped | 2020-01-25 | Compiled after data export & added compression to output |
| Rmd | 10a285b | Steve Ped | 2020-01-22 | Expanded description in index and tried reusing an image |
| html | 10a285b | Steve Ped | 2020-01-22 | Expanded description in index and tried reusing an image |
| html | b096ad9 | Steve Ped | 2020-01-21 | Recompiled index |
| Rmd | 01512da | Steve Ped | 2020-01-21 | Added initial DE analysis to index |
| Rmd | fbb6242 | Steve Ped | 2020-01-21 | Paused DE analysis |
| html | fbb6242 | Steve Ped | 2020-01-21 | Paused DE analysis |
| html | f154205 | Steve Ped | 2020-01-20 | Got rid of pointless warning |
| Rmd | bc12101 | Steve Ped | 2020-01-20 | Added bash pipeline |
| html | bc12101 | Steve Ped | 2020-01-20 | Added bash pipeline |
| html | f65bf66 | Steve Ped | 2020-01-20 | Removed License & updated text for PCA |
| Rmd | 39d0381 | Steve Ped | 2020-01-20 | Finished QC |
| html | 39d0381 | Steve Ped | 2020-01-20 | Finished QC |
| Rmd | acb4f8a | Steve Ped | 2020-01-19 | Start workflowr project. |
library(tidyverse)
library(tidygraph)
library(ggraph)samples <- read_csv("data/samples.csv") %>%
distinct(sampleName, .keep_all = TRUE) %>%
dplyr::select(sample = sampleName, sampleID, genotype) %>%
mutate(genotype = factor(genotype, levels = c("WT", "Het", "Hom")))This dataset is an analysis of RNASeq data from a 3-way comparison of WT zebrafish with Heterozygous mutants (psen2S4Ter/+) and Homozygous mutants psen2S4Ter/S4Ter. The psen2S4Ter mutant allele is expected to be a premature termination of the psen2 gene, but instead an alternate downstream start site resulted in a near full-length transcript with significant similarity to a conventional Early Onset Familial Alzhemier’s Disease mutation.
The expected comparisons were intended to be a three-way group comparison, however the final model was defined by fitting the wild-type samples, differences between heterozygotes and wild-type, followed by the difference between the two mutant genotypes
create_ring(3) %>%
mutate(
name = paste0(levels(samples$genotype), "\n(n = 4)"),
name = factor(name, levels = name)
) %>%
activate(edges) %>%
mutate(comparison = c("Het Vs WT", "Hom Vs Het", "Hom Vs WT")) %>%
dplyr::filter(comparison != "Hom Vs WT") %>%
ggraph(layout = "kk") +
geom_edge_link2(
aes(label = comparison),
angle_calc = "along",
label_dodge = unit(0.02, "npc"),
start_cap = circle(0.09, "npc"),
end_cap = circle(0.09, "npc"),
label_size = 5,
arrow = arrow(
length = unit(0.06, "npc"),
ends = "both",
type = "closed"
)
) +
geom_node_label(
aes(label = name, colour = name),
size = 5,
fill = rgb(1,1,1,0.7),
label.padding = unit(0.4, "lines")
) +
scale_y_continuous(expand = expand_scale(0.1)) +
scale_x_continuous(expand = expand_scale(0.1)) +
theme_void() +
theme(
legend.position = "none"
) 
All samples were female, 6 months old and raised in the same tank as a family, to minimise variability. This age represents sexual maturity and is expected to model a pre-symptomatic brain. Fish were all killed and genotyped by tail-clipping on 07-07-2016.
RNAseq was performed on total RNA (i.e. ribo-reduced) from whole brain tissue, with \(n=4\) samples in each group. Sequencing was performed by the sequencing facility at the Centre for Cancer Biology in Adelaide, using an Illimuna NextSeq. Reads were provided in as paired-end, 150bp reads.
- Bash Pipeline
- Quality Assesment
- Differential Expression Analysis
- Enrichment Analysis
devtools::session_info()─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 3.6.3 (2020-02-29)
os Ubuntu 18.04.4 LTS
system x86_64, linux-gnu
ui X11
language en_AU:en
collate en_AU.UTF-8
ctype en_AU.UTF-8
tz Australia/Adelaide
date 2020-04-02
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[3] /usr/lib/R/site-library
[4] /usr/lib/R/library