From fd38b76947f260fe3be768b2ad1be48da11d3093 Mon Sep 17 00:00:00 2001
From: Benedikt Venn <venn@bio.uni-kl.de>
Date: Wed, 22 Feb 2023 08:50:33 +0000
Subject: [PATCH] Update README.md
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# Carbon Availability Transcriptomics
-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).
+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. An x indicates triplicates measured at the respective time points._
|condition|-18 h (preheat)|2 h|4 h|8 h|24 h|reference|
|---|--|--|--|--|--|--|
-|25°C TAP|x|x| | |x|[Zhang et al. 2023](https://doi.org/10.1101/2022.12.04.519034)|
-|35°C TAP|x|x|x|x|x|[Zhang et al. 2022](https://doi.org/10.1038/s42003-022-03359-z)|
-|40°C TAP|x|x|x|x|x|[Zhang et al. 2022](https://doi.org/10.1038/s42003-022-03359-z)|
-|25°C nopump|x|x|x|x|x|[Zhang et al. 2023](https://doi.org/10.1101/2022.12.04.519034)|
-|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)|
+|25°C TAP|x|x| | |x|[Zhang et al. 2023](https://doi.org/10.1101/2022.12.04.519034)|
+|35°C TAP|x|x|x|x|x|[Zhang et al. 2022](https://doi.org/10.1038/s42003-022-03359-z)|
+|40°C TAP|x|x|x|x|x|[Zhang et al. 2022](https://doi.org/10.1038/s42003-022-03359-z)|
+|25°C nopump|x|x|x|x|x|[Zhang et al. 2023](https://doi.org/10.1101/2022.12.04.519034)|
+|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
@@ -33,22 +33,29 @@ References:
- Analysis:
- - Benedikt Venn, Lukas Weil, Kevin Schneider, David Zimmer & Timo Mühlhaus. (2022). fslaborg/FSharp.Stats. Zenodo. https://doi.org/10.5281/zenodo.6337056
+ - 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
+ - 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
+ - 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/
+
+ - BBDuk: https://sourceforge.net/projects/bbmap/
+
+ - Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 2015 Mar 9. doi: 10.1038/nmeth.3317.
+
+ - Ramirez F, Dundar F, Diehl S, Gruning BA, Manke T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 2014 Jul 1;42:W187-W191.
+
+ - Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30.
- 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
+ - 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
+ - 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
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