diff --git a/README.md b/README.md index 01ea7653bde5210857a2629efb8a287f0acab282..3a138c59e4211fd69f513e7777ad91d47efba60e 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,28 @@ Comparative analysis of both experiments were performed within this ARC. These i - visualization of all transcript signals and combined functional terms (Fig. 1) -<img src="https://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="80%"/> + +_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._ + + +References: + + - Analysis: + + - Benedikt Venn, Lukas Weil, Kevin Schneider, David Zimmer & Timo Mühlhaus. (2022). fslaborg/FSharp.Stats. Zenodo. https://doi.org/10.5281/zenodo.6337056 + + - Kevin Schneider, Lukas Weil, David Zimmer, Benedikt Venn & Timo Mühlhaus. (2022). CSBiology/BioFSharp. Zenodo. https://doi.org/10.5281/zenodo.6335372 + + - 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 + + - 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 + + - Data and annotation: + + - Merchant, S. S., Prochnik, S. E., Vallon, O., Harris, E. H., Karpowicz, S. J., Witman, G. B., … Grossman, A. R. (2007). The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions. Science, 318(5848), 245–250. https://doi.org/10.1126/science.1143609 + + - Zhang, N., Mattoon, E.M., McHargue, W. et al. Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii. Commun Biol 5, 460 (2022). https://doi.org/10.1038/s42003-022-03359-z -_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._ \ No newline at end of file diff --git a/runs/01_CountData/README.txt b/runs/01_CountData/README.md similarity index 100% rename from runs/01_CountData/README.txt rename to runs/01_CountData/README.md diff --git a/runs/02_Normalization/README.md b/runs/02_Normalization/README.md new file mode 100644 index 0000000000000000000000000000000000000000..bde131831a157a8bd0e3e0f379c3599bba5851cf --- /dev/null +++ b/runs/02_Normalization/README.md @@ -0,0 +1,3 @@ +## Normalization + +Merged count tables from TAP and nopump samples were normalized together for further comparison/analysis. \ No newline at end of file