DOI: 10.5061/dryad.nk98sf7q6
title: Data from: Transcriptomic signatures of social experience during early development in a highly social cichlid fish

description: The social environment encountered early during development can
 temporarily or permanently influence life history decisions and behaviour
 of individuals and correspondingly shape molecular pathways. In the highly
 social cichlid fish Neolamprologus pulcher, deprivation of brood care
 permanently affects social behaviour, and alters the expression of stress
 axis genes in juveniles and adults. It is unclear when gene expression
 patterns change during early life depending on social experience, and
 which genes are involved. We compared brain gene expression of N. pulcher
 at two time points during the social experience phase when juveniles were
 reared either with or without brood care, and one time point shortly
 afterwards. We compared (i) whole transcriptomes and (ii) expression of 79
 genes related to stress regulation, in order to define a neurogenomic
 state of stress for each fish. At developmental day 75, that is, after the
 social experience phase, 43 genes were down-regulated in fish having
 experienced social deprivation, while two genes involved in learning and
 memory and in post translational modifications of proteins (PTM),
 respectively, were up-regulated. Down-regulated genes were mainly
 associated with immunity, PTM and brain function. In contrast, during the
 experience phase no genes were differentially expressed when assessing the
 whole transcriptome. When focusing on the neurogenomic state associated
 with the stress response, we found that individuals from the two social
 treatments differed in how their brain gene expression profiles changed
 over developmental stages. Our results indicate that the early social
 environment influences the transcriptional activation in fish brains, both
 during and after an early social experience, possibly affecting
 plasticity, immune system function and stress axis regulation.
description: Additional information for data files added to the
 archive <br>
 <strong>Manuscript:</strong> Transcriptomic signatures of
 social experience during early development in a highly social cichlid
 fish <strong>Authors:</strong> Cecilia
 Nyman, Francois Olivier Hebert, Mathilde Bessert-Nettelbeck,
 Nadia-Aubin-Horth & Barbara Taborsky
 <strong><em>Files for analysis on differentially
 expressed genes:</em></strong> <strong>File:
 GeneExpressionN_pulcher_RNAseqpacbio.txt</strong><br>
 <em>File contains gene expression values for each fish. File used
 for gene expression analysis using the package ‘DESeq2’ of the statistical
 software ‘R’</em> First column: expressed
 genes<br> All other columns: gene expression of individual fish. ID
 of individual fish written on the first row in each column.
 <strong>File:
 Sample_information.txt</strong><br> <em>File contains
 information on treatment and the time the sample was collected for each
 fish. File used for gene expression analysis using the package ‘DESeq2’ of
 the statistical software ‘R’.</em> sample = ID of individual
 fish<br> treatment = fish reared with parents and a helper (plusF)
 or with siblings only (minusF)<br> timepoint = day in development,
 either day 46, 56 or 75<br> group = a new variable created by the
 combination of treatment and time point
 <strong><em>Files for NMDS
 analysis:</em></strong> <strong>File:
 nmds_scores_individuals.txt</strong><br> <em>File
 contains data for running two separate LMMs on the NMDS (non-linear
 multidimensional scaling) scores for each of the two dimensions (NMDS1 and
 NMDS2) using the package ‘lme4’ of the statistical software
 ‘R’</em> ind
 = ID of individual fish<br> group = a variable created by the
 combination of treatment and time point of sampling treat = treatment,
 fish reared with parents and a helper (s) or with siblings only (a) time =
 day in development, either day 46 (t46), 56 (t56) or 75 (t75)<br>
 tank = aquaria tank ID of individual fish<br> NMDS1 = NMDS1 scores
 for individual fish<br> NMDS2 = NMDS2 scores for individual
 fish