DOI: 10.5061/dryad.7d7wm3838
title: RNAseq of partially paralyzed zebrafish embryos at 5 days post-fertilization compared to normal siblings

description: Sofa potato (sop) is a mutant zebrafish line, whose synaptic transmission
 at the neuromuscular junction is absent due to a point mutation in the δ
 subunit gene of the acetylcholine receptor (AChR), leading to paralysis of
 its skeletal muscles. To explore genetic changes in embryos caused by the
 lack of synaptic transmission, we performed RNA-seq analysis of normal
 siblings (sop+/?) and sop homozygous embryos (sop-/-) at 5 days
 post-fertilization.
description: <em>Sofa potato</em> (sop) is a mutant zebrafish
 line, whose synaptic transmission at the neuromuscular junction is absent
 due to a point mutation in the δ subunit gene of the acetylcholine
 receptor (AChR), leading to paralysis of its skeletal muscles
 (doi:10.1523/jneurosci.0851-04.2004). To explore genetic changes in
 synapses caused by the lack of synaptic transmission, we performed RNA-seq
 analysis of normal siblings
 (<em>sop</em><sup>+/?</sup>) and <em>sop
 </em>homozygous embryos<em> (sop<sup>-/-</sup>)
 </em>at 5 dpf. <em>Sop<sup>-/-
 </sup></em>had an inducible wild type δ subunit gene, which
 was induced at 2 dpf resulting in partial paralysis
 (doi:10.1038/s41598-017-01900-3). Zebrafish embryos obtained from a cross
 of <em>sop</em><sup>+/-</sup> were separated into
 the paralyzed homozygous group
 (<em>sop</em><sup>-/-</sup>) and the swimming
 siblings (<em>sop</em><sup>+/+ </sup>or
 <em>sop</em><sup>+/-</sup>). Both groups were
 subjected to mifepristone to induce wild type delta subunit to partially
 rescue paralyzed fish. Total RNA was extracted from both groups (~10
 larvae in each) at 5 dpf using RNeasy Mini Kit (QIAGEN). Next-Generation
 sequencing and bioinformatics analysis was performed using TopHat and
 Cufflinks by Zymo Research. Read counts were ~56M and ~144M for
 <em>sop</em><sup>-/-</sup> and controls
 respectively.  
description: # RNAseq of partially paralyzed zebrafish embryos at 5 days
 post-fertilization compared to normal siblings
 [https://doi.org/10.5061/dryad.7d7wm3838](https://doi.org/10.5061/dryad.7d7wm3838) RNAseq data derived from zebrafish embryos at 5 days post fertilization, to compare the effect of paralysis. ## Description of the data and file structure Sofa potato (sop) is a mutant zebrafish line, whose synaptic transmission at the neuromuscular junction is absent due to a point mutation in the δ subunit gene of the acetylcholine receptor (AChR), leading to paralysis of its skeletal muscles (doi:10.1523/jneurosci.0851-04.2004). To explore genetic changes in synapses caused by the lack of synaptic transmission, we performed RNA-seq analysis of normal siblings (*sop*+/?) and sop *homozygous embryos* (sop-/-)  at 5 dpf. Sop-/-  had an inducible wild type δ subunit gene, which was induced at 2 dpf resulting in partial paralysis (doi:10.1038/s41598-017-01900-3). Zebrafish embryos obtained from a cross of *sop*+/- were separated into the paralyzed homozygous group (*sop*-/-) and the swimming siblings (*sop*+/+ or *sop*+/-). Both groups were subjected to mifepristone to induce wild type delta subunit to partially rescue paralyzed fish. Total RNA was extracted from both groups (~10 larvae in each) at 5 dpf using RNeasy Mini Kit (QIAGEN). Next-Generation sequencing and bioinformatics analysis was performed using TopHat and Cufflinks by Zymo Research. Read counts were ~56M and ~144M for *sop*-/- and controls respectively. Comparison of gene expression between control siblings (control) and partially paralyzed *sofa potato* mutants (mutant) are displayed in the Excel sheet. Uploaded file: Fig1A.xlsx.  Definitions in the file: 1. test id/gene id   :   A unique identifier describing the transcript, gene, primary transcript, or CDS being tested 2. gene   :   The gene_name(s) or gene_id(s) being tested 3. locus   :   Genomic coordinates for easy browsing to the genes or transcripts being tested. 4. sample 1  :   Control designates normally swimming zebrafish embryos at 5 days post fertilization. 5. sample 2   :   Mutant designates zebrafish embryos paralyzed due to a mutation in the acetylcholine receptors subunit gene at 5 days post fertilization 6. status   :   Can be one of OK (test successful), NOTEST (not enough alignments for testing), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents testing. 7. value 1 (FPKM - fragments per kilobase of transcript per million fragments mapped)   :   FPKM of the gene in sample 1 8. value 2 (FPKM)   :   FPKM of the gene in sample 2 9. log2(foldchange)   :   The (base2) log of the fold change of samples 2/1 10. test stat   :   The value of the test statistic used to compute significance of the observed change in FPKM 11. p value   :   The uncorrected *p*-value of the test statistic 12. q value   :   The FDR-adjusted *p*-value of the test statistic 13. significant   :   Can be either "yes" or "no", depending on whether *p *is greater than the FDR after Benjamini-Hochberg correction for multiple- testing References Ono F, Mandel G, Brehm P. Acetylcholine Receptors Direct Rapsyn Clusters to the Neuromuscular Synapse in Zebrafish. Journal of Neuroscience. 2004;24: 5475–5481. doi:10.1523/jneurosci.0851-04.2004 Mott M, Luna VM, Park J-Y, Downes GB, Epley K, Ono F. Expressing acetylcholine receptors after innervation suppresses spontaneous vesicle release and causes muscle fatigue. Scientific reports. 2017; 1–8. doi:10.1038/s41598-017-01900-3