From a24e4e6ea6ef8958f988ed70718c58a9b338ba87 Mon Sep 17 00:00:00 2001
From: Benedikt Venn <venn@bio.uni-kl.de>
Date: Mon, 30 Jan 2023 13:51:37 +0100
Subject: [PATCH] update readme
---
README.md | 15 +++++++++------
runs/04_StatisticalAnalysis/README.md | 2 ++
2 files changed, 11 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index 3a138c59..482ec6ec 100644
--- a/README.md
+++ b/README.md
@@ -16,15 +16,15 @@ _Table 1: Sampling schema for Transcriptomics analysis. Three biological replica
Comparative analysis of both experiments were performed within this ARC. These include
- - combined normalization
+ 1. combined normalization
- - statistical analysis
+ 2. statistical analysis
- - enrichment studies
-
- - visualization of all transcript signals and combined functional terms (Fig. 1)
+ 3. enrichment studies
+
+ 4. visualization of all transcript signals and combined functional terms (Fig. 1)
-<img src="https://git.nfdi4plants.org/lux/carbon-availability-transcriptomics-chlamy/-/raw/main/studies/HeatstressExperiment/resources/Figure01.png" alt="Signal" width="80%"/>
+<img src="https://git.nfdi4plants.org/lux/carbon-availability-transcriptomics-chlamy/-/raw/main/studies/HeatstressExperiment/resources/Figure01.png" alt="Signal" width="100%"/>
_Figure 1: Example of generated figures. **(A)** Exemplary visualization of the normalized counts of the HSP70C transcript. A clear separation of the different temperature kinetics is visible. While the initial level is comparable for all time courses after heat onset of 35°C transcript counts increase strongly while the 25°C signal seems constant. Transcript counts in both 40°C experiments decreased during the first 4 hours of treatment. After 8 hours of heat stress the behaviour of temperature-regulated signals change to medium specific effects. Cells living in low-acetate media show distinct reduction of HSP70C transcripts while TAP-samples settle approximately at prior-heat levels. **(B)** Heatmap representation of (A). **(C)** Transcript signals that belong to the functional term "intraflagellar transport.IFT particle protein.complex B" are visualized as z-scores. Since there was no measurement for TAP-25°C this panel remains empty (lower left). Because z-scores may distort signals that did not change at all, a ANOVA was performed to separate constant transcript from transcripts that showed differential expression within their time courses. Red shadings indicate a global change of the transcript counts. Blue/grey signals can be considered as constant and have less relevance for the shown kinetics. As seen most transcripts show no response at 25°C but show distinct patterns for 35°C and 40°C respectively. The response shape is solely dependent on the applied temperature and is not influenced by the media the cells are grown in. While for 35°C the transcripts show a strong decrease within the first two hours and a strong increase during the last period, for 40°C samples the transcripts remain constant for the first 2 hours and show no strong increase for the last time point._
@@ -39,6 +39,9 @@ References:
- Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014). https://doi.org/10.1186/s13059-014-0550-8
+ - Andrews, S. (n.d.). FastQC A Quality Control tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+
+
- Visualization:
- Schneider K, Venn B and Mühlhaus T. Plotly.NET: A fully featured charting library for .NET programming languages [version 1; peer review: awaiting peer review]. F1000Research 2022, 11:1094 (https://doi.org/10.12688/f1000research.123971.1
diff --git a/runs/04_StatisticalAnalysis/README.md b/runs/04_StatisticalAnalysis/README.md
index 5a852ded..25dc98e7 100644
--- a/runs/04_StatisticalAnalysis/README.md
+++ b/runs/04_StatisticalAnalysis/README.md
@@ -1,5 +1,7 @@
Please decompress the plots.zip folder on a local harddrive. if analysisSummary.xlsx is located in the same folder as /plots the links in the first column of the excel file should work.
├───04_StatisticalAnalysis
+
│ analysisSummary.xlsx
+
│ plots
--
GitLab