Computational protocol: Pre‐mRNA splicing is modulated by antifungal drugs in the filamentous fungus Neurospora crassa

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Protocol publication

[…] Publicly available RNAseq data (next‐generation RNA sequencing technologies) from the Sequence Read Archive at the NCBI database (http://www.ncbi.nlm.nih.gov/sra) was used to quantify intron retention events in N. crassa. Seven RNAseq experiments for N. crassa wild‐type strains grown on glucose (GEO: GSM1238604 and GSM1238606), xylose (GEO: GSM1238609), arabinose (GEO: GSM1238602 and GSM1238597), sucrose (GEO: GSM899613), and cellulose (Avicel, GEO: GSM899607) were used. For intron retention quantification, SRA files were downloaded from the database and converted to fastq format using the SRA toolkit. Reads were then aligned to fasta files containing sequences of 50 nt representing each exon–intron boundary for the genes of interest (KEGG: NCU04303, NCU08726, and NCU05999) using Bowtie , . The number of reads mapped at each boundary was used to estimate the prevalence of intron retention events in each gene. […]

Pipeline specifications

Software tools SRA Toolkit, Bowtie
Databases SRA KEGG
Application RNA-seq analysis
Organisms Neurospora crassa
Chemicals Amphotericin B, Ketoconazole, Phosphates