Computational protocol: Whole organism transcriptome analysis of zebrafish models of Bardet-Biedl Syndrome and Alström Syndrome provides mechanistic insight into shared and divergent phenotypes

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Protocol publication

[…] Sequenced reads were aligned to the zebrafish genomes (Zv10) using TopHat []. Gene expression levels (read counts) were calculated using HTseq [] based on ENSEMBL gene annotations []. The zebrafish datasets were then normalized using reads per kilobase per million reads (RPKM). An average of 28,700 features were detected as expressed in each sample set. Replicate analysis and differentially expressed genes were determined using DEGseq []. Both alms1 and bbs1 knockdowns were compared to the control, cutoffs of false discovery rate (FDR) <0.05 and p value <0.05 were used to identify genes with significant changes in expression. Primary data analysis was performed at the Institute for Genome Sciences of the University of Maryland, School of Medicine (IGS). Sequence data for samples is publicly available through the NCBI Sequence Read Archive (SRA), Submission ID “University of Maryland BBS Alstrom Zebrafish RNA-Seq”. […]

Pipeline specifications

Software tools TopHat, HTSeq, DEGseq
Application RNA-seq analysis
Organisms Danio rerio
Diseases Bardet-Biedl Syndrome, Genetic Diseases, Inborn
Chemicals Calcium