Computational protocol: Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish

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Protocol publication

[…] Image analysis and base calling were performed with Illumina's Real Time Analysis v1.12 software. Files were demultiplexed of indexed reads and generated in FASTQ format using Illumina's CASAVA v1.8. software. Reads were removed that did not pass Illumina's base call quality threshold. Reads were aligned to zebrafish genome build Zv9 release 63, using TopHat 1.4 (). SAMtools v0.1.18 () was used to sort and index the TopHat alignments such that they could be visualized in the Integrative Genomics Viewer (). The gene expression profiles of control-MO;prdm1+/+ versus control-MO;prdm1−/−; pbx2/4-MO;prdm1+/+; and pbx2/4-MO;prdm1−/− embryos were compared using the Bioconductor package edgeR (). To include reads that mapped to multiple homologs in the zebrafish genome, including the myosin heavy chain genes, reads with multiple hits on the genome were kept, and each hit received a fractional count equal to one over the number of hits. Venn diagrams were generated using BioVenn (). Data have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE45532. […]

Pipeline specifications

Software tools BaseSpace, TopHat, SAMtools, IGV, edgeR, BioVenn
Databases GEO
Application RNA-seq analysis
Organisms Danio rerio