diff --git a/README.md b/README.md index 357ff9b0b4d1017446c6f089e8de9f0be0c76f58..01ea7653bde5210857a2629efb8a287f0acab282 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ Chlamydomonas reinhardtii CC-1690 was grown in bioreactors. When the cells reached a non-stationary density, the acetate supply was stopped and the medium was kept at 25°C (control) or heated to 35 °C and 40 °C. Additionally to a preheat sample, four further samples were taken as triplicates after 2h, 4h, 8h, and 24h of heat treatment (nopump samples). The samples were analysed with NGS. In [Zhang et al 2022](https://doi.org/10.1038/s42003-022-03359-z) samples were taken at the same time points for 35°C and 40°C but with constant nutrient supply (TAP samples). -_Table 1: Sampling schema for Transcriptomics analysis. Three biological replicates were measured._ +_Table 1: Sampling schema for Transcriptomics analysis. Three biological replicates were measured. An x indicates triplicates measured at the respective time points._ |condition|-18 h (preheat)|2 h|4 h|8 h|24 h|reference| |---|--|--|--|--|--|--| @@ -14,3 +14,16 @@ _Table 1: Sampling schema for Transcriptomics analysis. Three biological replica |35°C nopump|x|x|x|x|x|[Zhang et al. 2023](https://doi.org/10.1101/2022.12.04.519034)| |40°C nopump|x|x|x|x|x|[Zhang et al. 2023](https://doi.org/10.1101/2022.12.04.519034)| +Comparative analysis of both experiments were performed within this ARC. These include + + - combined normalization + + - statistical analysis + + - enrichment studies + + - 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%"/> + +_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.txt new file mode 100644 index 0000000000000000000000000000000000000000..3e37c08e00f6e844d58b4638bdf8be390029feff --- /dev/null +++ b/runs/01_CountData/README.txt @@ -0,0 +1 @@ +Counts measured in Zhang 2022 located in `runs\01_CountData\Zhang2022` were merged with counts measured in Zhang 2023 located at `assays\Transcriptomics\dataset`. \ No newline at end of file diff --git a/runs/03_PCA/README.md b/runs/03_PCA/README.md index 3c1f7c3d5bcea72f7fed84838bc0306fc86e87e3..b395d1ce12148ef2af3193776fef88799b119c5d 100644 --- a/runs/03_PCA/README.md +++ b/runs/03_PCA/README.md @@ -2,7 +2,7 @@ Note: - - TAP samples were taken at more time points. 1, 5, 6, 7, and 9 correspond to the same timepoints as measured in nopump samples + - TAP samples were taken at more time points than nopump samples. 1, 5, 6, 7, and 9 correspond to the same timepoints as measured in nopump samples. |sample names|medium|temperature|description| |--|--|--|--| diff --git a/runs/04_StatisticalAnalysis/README.md b/runs/04_StatisticalAnalysis/README.md index 6e14fc7ae9d53ecf5a5ef0092683ba72ad58138a..5a852dedfa8621c137abda7d43e78e566604a009 100644 --- a/runs/04_StatisticalAnalysis/README.md +++ b/runs/04_StatisticalAnalysis/README.md @@ -1,7 +1,5 @@ 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.zip -│ README.md \ No newline at end of file +│ plots diff --git a/runs/06_FunctionalSetFigures/README.md b/runs/06_FunctionalSetFigures/README.md index 0268d35f9c399eb439750485dfdd1145640b2280..8a7ef608ee14f0aee5bbc2357e5304e9a60006cf 100644 --- a/runs/06_FunctionalSetFigures/README.md +++ b/runs/06_FunctionalSetFigures/README.md @@ -1,12 +1,14 @@ +## Functional set visualization + CreIdentifier were grouped by (expanded) MapMan functional annotation. To test whether a signal over time differed at all a ANOVA was performed. Significant signals are colored in red-shades, unsignificant signals in blue/grey. -Values: +### Values: _LFC_: log2 fold changes were determined in respect to the preheat samples -_zScores: zScores of the signals were determined +_zScores_: zScores of the signals were determined -Spacing: +### Spacing: _equally_: every time point is equally spaced diff --git a/studies/HeatstressExperiment/resources/Figure01.png b/studies/HeatstressExperiment/resources/Figure01.png new file mode 100644 index 0000000000000000000000000000000000000000..c9d3735ed42cf70ee2b44f7b29158faac978d553 Binary files /dev/null and b/studies/HeatstressExperiment/resources/Figure01.png differ