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