DOI: 10.5061/dryad.4g048
title: Data from: Unmapped sequencing reads identify additional candidate genes linked to magnetoreception in rainbow trout

description: A recent study identified candidate genes linked to magnetoreception in
 rainbow trout (Oncorhynchus mykiss) by sequencing transcriptomes from the
 brains of fish exposed to a magnetic pulse. However, the discovery of
 these candidate genes was limited to sequences that aligned to the
 reference genome. The unaligned, or unmapped, sequences may yet contain
 valuable information resulting from regions missing, misassembled, or
 divergent from the reference. Using the available sequencing data from the
 trout brain transcriptomes, we assembled &gt;27 million unmapped
 sequences (5.8% of total sequences) into 45,142 contigs and identified 12
 differentially expressed contigs as a result of exposure to a pulsed
 magnetic field. These contigs encoded a putative superoxide dismutase – a
 protein necessary to prevent oxidative damage – and collagen alpha-1 type
 II – a structural protein important for the development and integrity of
 the retina. These genes were consistent with the previous study suggesting
 an effect of the magnetic pulse on oxidative consequences of free iron and
 on non-visual encephalic photoreceptors. Our results demonstrate the
 utility of assembling unmapped sequencing reads in studies of gene
 expression and identify additional candidate genes associated with a
 magnetic sense in trout.
description: Cleaned
 AssemblyThe file contains the
 filtered de novo assembly (TPM &gt; 1) produced from the unmapped reads
 using Trinity. There are 45,142 contigs present.Trinity_TPM1.fastaBlast2GO Annotation fileThis file contains the entire database created using Blast2GO to annotate all the contigs from the filtered unmapped reads assembly (Trinity_TPM1.fasta).Trinity_TPM1.b2gBlast2Go Annotations (Text format)This file contains a summary of the annotation using Blast2GO in text format for all the contigs from the filtered unmapped reads assembly (Trinity_TPM1.fasta).Full-annotation.tsvExpression MatrixThis spreadsheet contains the raw expression level (counts) in each of the 10 libraries analyzed for differential expression. The first row lists the names of the 10 RNA-seq libraries (see 'Note' in README). Raw counts were produced using RSEM v1.3.0.Expression-matrix.tsvSample Matrix for EdgeRThis spreadsheet contains only two columns. The first column is the group (control or pulsed) and the second the library ID (4,7,9,10,11,12,13,14,15,16). This file is only used by EdgeR to analyze differential expression.samples.tsvDifferential Expression ResultsThis spreadsheet contains the results from calculations of differential expression for each contig. Only 39,714 contigs were assessed for differential expression. The columns are: Contig_name; sampleA; sampleB; LogFC (fold change); logCPM (counts per million); P-value; FDR (false discovery rate).DE-table.tsvRaw AssemblyThis file contains the raw, de novo assembly produced from the unmapped reads using Trinity. There are 104,588 contigs present.Trinity.fastaC1 Unmapped ReadsC1.fastq.gzC2 Unmapped ReadsC2.fastq.gzC3 Unmapped ReadsC3.fastq.gzC4 Unmapped ReadsC4.fastq.gzC9 Unmapped ReadsC9.fastq.gzC10 Unmapped ReadsC10.fastq.gzC11 Unmapped ReadsC11.fastq.gzC12 Unmapped ReadsC12.fastq.gzP5 Unmapped ReadsP5.fastq.gzP6 Unmapped ReadsP6.fastq.gzP7 Unmapped ReadsP7.fastq.gzP8 Unmapped ReadsP8.fastq.gzP13 Unmapped ReadsP13.fastq.gzP14 Unmapped ReadsP14.fastq.gzP15 Unmapped ReadsP15.fastq.gzP16 Unmapped ReadsP16.fastq.gzREADME fileThis file contains a complete description of all files in this data archive, including md5 tags, file formats and all code used to generate the data in this study.