Comparative transcriptomics of fungi Group Nicotiana Daan van Vliet, Dou Hu, Joost de Jong, Krista...
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![Page 1: Comparative transcriptomics of fungi Group Nicotiana Daan van Vliet, Dou Hu, Joost de Jong, Krista Kokki.](https://reader036.fdocuments.us/reader036/viewer/2022083119/5a4d1b107f8b9ab05998eaf1/html5/thumbnails/1.jpg)
Comparative transcriptomics
of fungi
Group NicotianaDaan van Vliet, Dou Hu, Joost de Jong, Krista Kokki
![Page 2: Comparative transcriptomics of fungi Group Nicotiana Daan van Vliet, Dou Hu, Joost de Jong, Krista Kokki.](https://reader036.fdocuments.us/reader036/viewer/2022083119/5a4d1b107f8b9ab05998eaf1/html5/thumbnails/2.jpg)
Research objectiveTo study differences in gene expression in related fungi species
Studies species:- Reference genome- RNA reads > 100 bp- Preferably: Paired-end- Related species (or at least: single-celled,
eukaryotic) - Similar conditions
![Page 3: Comparative transcriptomics of fungi Group Nicotiana Daan van Vliet, Dou Hu, Joost de Jong, Krista Kokki.](https://reader036.fdocuments.us/reader036/viewer/2022083119/5a4d1b107f8b9ab05998eaf1/html5/thumbnails/3.jpg)
Data generation
- Cleaning reads: FastQC (cut value: 25) - Mapping reads: TopHat- Assemble and quantify transcripts:
Cufflinks- Extracting the transcripts: gffread
![Page 4: Comparative transcriptomics of fungi Group Nicotiana Daan van Vliet, Dou Hu, Joost de Jong, Krista Kokki.](https://reader036.fdocuments.us/reader036/viewer/2022083119/5a4d1b107f8b9ab05998eaf1/html5/thumbnails/4.jpg)
Data processing
Extract top 100 expressed transcripts- Unix command pipeline within Perl (sort,
head)
Determining gc-content and length of transcripts - Perl subroutines
![Page 5: Comparative transcriptomics of fungi Group Nicotiana Daan van Vliet, Dou Hu, Joost de Jong, Krista Kokki.](https://reader036.fdocuments.us/reader036/viewer/2022083119/5a4d1b107f8b9ab05998eaf1/html5/thumbnails/5.jpg)
Data processingDetermine intron length- Perl: length (transcript) – length of the exons (specified in
Cufflinks output)
Codon usage- Perl: loop to analyse codon by codon (within each transcript)- Count frequencies of codons, store in an array- Calculate codon usage index (such as the effective number
of codons, NC)
Validation- Run scripts on small, example datasets
![Page 6: Comparative transcriptomics of fungi Group Nicotiana Daan van Vliet, Dou Hu, Joost de Jong, Krista Kokki.](https://reader036.fdocuments.us/reader036/viewer/2022083119/5a4d1b107f8b9ab05998eaf1/html5/thumbnails/6.jpg)
Statistical analysis and visualization
Use R to determine and visualize correlation coefficients
Expression level
Species 1 Species 2
Transcript length 0.25* -0.10*CG-content 0.00 0.02Codon usage bias 0.30* -0.32*