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Data from: Transcriptomic signatures of social experience during early development in a highly social cichlid fish

Citation

Nyman, Cecilia et al. (2019), Data from: Transcriptomic signatures of social experience during early development in a highly social cichlid fish, Dryad, Dataset, https://doi.org/10.5061/dryad.nk98sf7q6

Abstract

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.

Usage Notes

Additional information for data files added to the archive


Manuscript: Transcriptomic signatures of social experience during early development in a highly social cichlid fish

Authors: Cecilia Nyman, Francois Olivier Hebert, Mathilde Bessert-Nettelbeck, Nadia-Aubin-Horth & Barbara Taborsky

Files for analysis on differentially expressed genes:

File: GeneExpressionN_pulcher_RNAseqpacbio.txt
File contains gene expression values for each fish. File used for gene expression analysis using the package ‘DESeq2’ of the statistical software ‘R’

First column: expressed genes
All other columns: gene expression of individual fish. ID of individual fish written on the first row in each column.

File: Sample_information.txt
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’.

sample = ID of individual fish
treatment = fish reared with parents and a helper (plusF) or with siblings only (minusF)
timepoint = day in development, either day 46, 56 or 75
group = a new variable created by the combination of treatment and time point

Files for NMDS analysis:

File: nmds_scores_individuals.txt
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’

ind = ID of individual fish
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)
tank = aquaria tank ID of individual fish
NMDS1 = NMDS1 scores for individual fish
NMDS2 = NMDS2 scores for individual fish