10.5061/DRYAD.73B86
Fitak, Robert R.
Duke University
Wheeler, Benjamin R.
Duke University
Ernst, David A.
University of North Carolina
Lohmann, Kenneth J.
University of North Carolina
Johnsen, Sonke
Duke University
Data from: Candidate genes mediating magnetoreception in rainbow trout
(Oncorhynchus mykiss)
Dryad
dataset
2017
Magnetite
magnetic pulse
Ferritin
Oncorhynchus mykiss
2017-03-30T18:41:18Z
2017-03-30T18:41:18Z
en
https://doi.org/10.1098/rsbl.2017.0142
18839058900 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Diverse animals use Earth's magnetic field in orientation and
navigation, but little is known about the molecular mechanisms that
underlie magnetoreception. Recent studies have focused on two
possibilities: (i) magnetite-based receptors; and (ii) biochemical
reactions involving radical pairs. We used RNA sequencing to examine gene
expression in the brain of rainbow trout (Oncorhynchus mykiss) after
exposure to a magnetic pulse known to disrupt magnetic orientation
behaviour. We identified 181 differentially expressed genes, including
increased expression of six copies of the frim gene, which encodes a
subunit of the universal iron-binding and trafficking protein ferritin.
Functions linked to the oxidative effects of free iron (e.g.
oxidoreductase activity, transition metal ion binding, mitochondrial
oxidative phosphorylation) were also affected. These results are
consistent with the hypothesis that a magnetic pulse alters or damages
magnetite-based receptors and/or other iron-containing structures, which
are subsequently repaired or replaced through processes involving
ferritin. Additionally, some genes that function in the development and
repair of photoreceptive structures (e.g. crggm3, purp, prl, gcip, crabp1
and pax6) were also differentially expressed, raising the possibility that
a magnetic pulse might affect structures and processes unrelated to
magnetite-based magnetoreceptors.
Expression Data from CUFFLINKSThis spreadsheet contains the normalized
expression level (FPKM) in each of the 10 sequenced libraries, in addition
to the expression for each treatment (control vs pulsed) and the
expression ratio (log2_fold_change). The “Description” for each protein
includes all annotated GO terms for that protein from BLAST2GO. All
protein IDs are from the Trout Genome Browser –
www.genoscope.cns.fr/troutAll_expression-data.csvC4 Alignment (BAM)
fileThis is the alignment (BAM) file for control group sample C4 created
by mapping the trimmed reads using STAR v2.5.0. Md5 tag =
d194fb49262e369e0d143ce0e4cfd0ccC4.mapping-Aligned.sortedByCoord.out.bamC9
Alignment (BAM) fileThis is the alignment (BAM) file for control group
sample C9 created by mapping the trimmed reads using STAR v2.5.0. Md5 tag
=
2fc8f6ee81649a6a772f82c720e7a9dbC9.mapping-Aligned.sortedByCoord.out.bamC10 Alignment (BAM) fileThis is the alignment (BAM) file for control group sample C10 created by mapping the trimmed reads using STAR v2.5.0. Md5 tag = 7701d1f77208e03c4fd850d8f22c0775C10.mapping-Aligned.sortedByCoord.out.bamC11 Alignment (BAM) fileThis is the alignment (BAM) file for control group sample C11 created by mapping the trimmed reads using STAR v2.5.0. Md5 tag = b5c3d65db71162aa1b9d7646fa2823a9C11.mapping-Aligned.sortedByCoord.out.bamC12 Alignment (BAM) fileThis is the alignment (BAM) file for control group sample C12 created by mapping the trimmed reads using STAR v2.5.0. Md5 tag = 5e700bf725e2f12fade6fc8e925ab676C12.mapping-Aligned.sortedByCoord.out.bamP7 Alignment (BAM) fileThis is the alignment (BAM) file for pulsed group sample P7 created by mapping the trimmed reads using STAR v2.5.0. Md5 tag = 6336249f9067b0ddc65d0f9a144ff7beP7.mapping-Aligned.sortedByCoord.out.bamP13 Alignment (BAM) fileThis is the alignment (BAM) file for pulsed group sample P13 created by mapping the trimmed reads using STAR v2.5.0. Md5 tag = 2e1d24aad1707dc3df1e1b43e51e53c2P13.mapping-Aligned.sortedByCoord.out.bamP14 Alignment (BAM) fileThis is the alignment (BAM) file for pulsed group sample P14 created by mapping the trimmed reads using STAR v2.5.0. Md5 tag = 7eeb1f4452727cf41422cacc3e9f317cP14.mapping-Aligned.sortedByCoord.out.bamP15 Alignment (BAM) fileThis is the alignment (BAM) file for pulsed group sample P15 created by mapping the trimmed reads using STAR v2.5.0. Md5 tag = c17e282388161b6e7e48305ec8ae421fP15.mapping-Aligned.sortedByCoord.out.bamP16 Alignment (BAM) fileThis is the alignment (BAM) file for pulsed group sample P16 created by mapping the trimmed reads using STAR v2.5.0. Md5 tag = 7be88352777672f3f755e2511b267fbfP16.mapping-Aligned.sortedByCoord.out.bamO. mykiss Blast2GO databaseThis file contains the complete de novo annotation of all protein-coding genes in the trout genome using Blast2GO. This file can only be opened using Blast2GO, and the user must request a license (free) from the supplier.Omykiss.b2gO. mykiss GO annotationThe file is a table summarizing the Blast2GO output. See README.txt for more information.O_mykiss.blast2go.annot.csvREADME fileA description of the contents of this data archive.