Impact of short photoperiod length on smoltification (RNAseq)
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Salmo salar
SUBMITTER: Line Røsæg
PROVIDER: E-MTAB-10526 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The anadromous Atlantic salmon undergo preparatory physiological transformations before seawater entry, referred to as smoltification. Little is known about the photoperiod-influence and genome regulatory processes driving smoltification such as the large scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. To shed light on this, we performed a smoltification trial using contrasting photoperiod regimes and generate a transcriptome data from livers throughout smoltification and after seawater transfer. In this experiment two groups of Atlantic salmon were reared for a total of 46 weeks from the parr stage, through smoltification, and seawater transfer. After 21 week from first feeding, the experiment group was given artificial winter photoperiod (8 hours light, 16 hours dark) for 8 weeks to induce smoltification before returning to constant light. The second control group received constant light throughout the experiment. Liver tissue was sampled from individuals first at week 1, 21 weeks after first feeding, then again at week 10, after the winter period, at week 19, after the expected smoltification time, and lastly at week 25, after transfer to seawater.
2022-05-16 | E-MTAB-11746 | biostudies-arrayexpress
Project description:The experiment is designed to assess the impact of winter length on epigenetic status of key genes related to smoltification. Transferring fish from constant light (LL) to short photoperiod (SP) for different durations and then returning to constant light (LL) for 8 weeks to stimulate smoltification. Three histone marks were assessed: H3K4me3, H3K27me3 and H3K27ac.
2023-10-27 | E-MTAB-11091 | biostudies-arrayexpress
Project description:The anadromous Atlantic salmon undergo preparatory physiological transformations before seawater entry, referred to as smoltification. Little is known about the photoperiod-influence and genome regulatory processes driving smoltification such as the large scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. To shed light on this, we performed a smoltification trial using contrasting photoperiod regimes and generate ATAC-seq data from livers throughout smoltification and after seawater transfer to assess the differences in chromatin accessibility. In this experiment Atlantic salmon were reared for a total of 46 weeks from the parr stage, through smoltification, and seawater transfer. After 21 week from first feeding, the group was given artificial winter photoperiod (8 hours light, 16 hours dark) for 8 weeks to induce smoltification before returning to constant light. Liver tissue was sampled from individuals first at week 1, 21 weeks after first feeding, then again at week 10, after the winter period, at week 19, after the expected smoltification time, and lastly at week 25, after transfer to seawater.
2024-02-02 | E-MTAB-13743 | biostudies-arrayexpress
Project description:Microarray analysis on Brachypodium distachyon seedlings was performed to determine the response of the transcriptome to changes in ambient temperature, including identification of marker genes that were up-regulated or down-regulated by a moderate increase in growth temperature. Wild-type Brachypodium (Bd21) seedlings were grown on MSR63 media without sucrose (Alves et al. 2009 Nature Protocols vol. 4 pp 638-649) in a short-day photoperiod (14 hr light/ 10 hr dark) at 17 ºC. As the third leaf was emerging, plants were transferred to 12 ºC for 48 hrs. Plants were then maintained at 12 ºC or transferred to one of two temperature treatments: constant 22 ºC or constant 27 ºC. Samples were collected before the shift (0 hr) and at 2 hr and 24 hr after the shift and immediately frozen in liquid nitrogen. For each harvest, two to three replicates were collected that each contained 3 seedlings.
2013-06-07 | E-MEXP-3918 | biostudies-arrayexpress
Project description:The F5 generation of a wild-caught population of zebrafish (Danio rerio) from Mymensingh, Bangladesh, were used in this study. Replicate experiments were carried out with adult male fish aged 9 months. Each group was maintained in a 50L tank at 27M-11.5M-:C and 12:12h dark:light photoperiod and fed bloodworms (Ocean NutritionM-^Y, Belgium) to satiety for one week. The experimental protocol involved fasting fish for 7 days and subsequent refeeding a single meal of bloodworms delivered over a 3h period, after which any uneaten food was removed from the tank. Seven fish were sampled at -156, -24, 0 (prior to the meal), 0.75, 3, 6, 7.5, 9, 11, 24, 36h and killed humanely by an overdose of ethyl 3-aminobenzoate methanesulfonate salt (MS-222). Six samples from the 0, 3, and 6h time-points were used in the microarray hybridization.
2011-03-11 | E-MEXP-2887 | biostudies-arrayexpress
Project description:In this study, we used whole genome comparative oligonucleotide microarrays to investigate the brain transcriptomic response to predator cues using the threespine stickleback, Gasteroteus aculeatus. We showed that exposure to olfactory, visual and tactile cues of a predator (rainbow trout, Oncorhynchus mykiss) for six days resulted in subtle but significant transcriptomic changes in the brain of sticklebacks. Gene functional analysis and gene ontology (GO) enrichment revealed that the majority of the transcripts differentially expressed between the fish exposed to predator cues and the control group are primarily related to antigen processing and presentation (involving primarily the major histocompatibility complex (MHC)), transmission of synaptic signals, brain metabolic processes, gene regulation, or visual perception. Pathway analysis identified synaptic long-term depression, RAN signaling, relaxin signaling and phototransduction as the top four pathways that were over-represented. Adult fish were placed in six different 26L tanks with three fish per tank in a partially recirculating flow-through system. Half of the tanks were assigned to the control group and the other half to the experimental group.10 samples were selected for microarray analysis. The ten samples comprised five biological replicates in the experimental group (fish exposed to predator cues) and five biological replicates in the control group (fish not exposed to predator cues), and were evenly distributed across tanks. The cDNA labeling (single color), hybridization, washing and scanning steps were performed in the NimbleGen microarray gene expression service department.
2011-04-24 | E-GEOD-21599 | biostudies-arrayexpress
Project description:Grey mouse lemurs (Microcebus murinus) are a primate species, which exhibits strong physiological seasonality in response to environmental energetic constraint. They notably accumulate large amounts of lipid reserves during early winter, which are thereafter mobilized during late winter, when food availability is very low. In addition, they develop glucose intolerance in late winter only. To decipher how the hepatic mechanisms may support such metabolic flexibility, we analyzed the liver proteome of captive lemurs, which seasonal regulations of metabolism and reproduction are comparable to their wild counterparts, during the phases of either constitution or use of fat reserves.
2022-05-04 | PXD030198 | Pride
Project description:This experiment is intended to provide information about transcriptional changes in the gill of Atlantic salmon during smoltification, in comparison with juvenile salmon not given the appropriate photoperiodic stimuli. Also, transcriptional changes due to osmotic stress (24H salt water challenged) will be recorded. This to better understand the transformation of the gill from a fresh water-type to a salt water-type, and possibly identify novel and important genes that are dependent upon a specific photoperiodic history for their expression. Additionally the data can be used to observe the shift in salt water response as the juvenile salmon goes through smoltification. Experimental workflow: All fish started on 24H light (LL), after one week, half of the fish were moved to short photoperiod (8:16, SP). The rest remained on LL throughout. After eight weeks, half of the fish on short photoperiod were moved back onto 24H light (SPLL). Remaining fish continued under 8:16. After another eight weeks the experiment was ended. Fish were sampled on days 0, 32, 53, 68, 89 and 110. On each sampling occasion fish were sampled directly from fresh water (FW), and from a 24H salt water (SW) stay, transferred the previous day. Weight and length was noted. Gill tissue was the taken and placed in RNAlater. Additionally plasma for measuring hypoosmoregulatory capacity was taken.
2019-09-12 | E-MTAB-8276 | biostudies-arrayexpress
Project description:Aphid adaptation to harsh winter conditions is illustrated by an alternation of their reproductive mode. Aphids detect photoperiod shortening by sensing the length of the night and switch from viviparous parthenogenesis in spring and summer, to oviparous sexual reproduction in autumn. The photoperiodic signal is transduced from the head to the reproductive tract to change the fate of the future oocytes from mitotic diploid embryogenesis to haploid formation of gametes. Because of viviparous parthenogenesis, the whole process takes place in three consecutive generations. To understand the molecular basis of the switch in the reproductive mode, a transcriptomic approach was used to detect significantly regulated transcripts in the heads of the pea aphid Acyrthosiphon pisum. The transcriptomic profiles of the heads of the first generation were slightly affected by photoperiod shortening. This suggests that trans-generation signaling does not occur between the grand-mothers and the viviparous embryos they contain. By analogy, many of the genes regulated in the heads of the second generation are implicated in visual functions, photoreception and cuticle structure. The modification of the cuticle could decrease the storage of N-β-alanyldopamine and provoke an increase in free dopamine concentration. Based in results in Drosophila, modification of the insulin pathway could cause a decrease of juvenile hormones in short-day reared aphids. Biological material for microarray experiments was prepared under two dayly photoperiodic regimes both at constant temperature of 18°C: i) âShort Nightâ (SN) at 16h of light and ii) âLong Nightâ (LN) at 12h of light to induce the production of sexual morphs. To initiate the experiment, two groups of 105 L3 larvae were placed either under SN or LN condition. This corresponds to generation G0. At the middle of the photophase, 25 individual were frozen when they had reached both the L4 and the wingless adult (WA) stages, in the two photoperiod conditions. The 55 remaining WA individuals (still divided in two groups) were left on 55 plants to lay their offspring: one larva of the 1st stage (L1) was kept per WA. This larva was selected among the 20 first born larvae. This is the generation G1. At the middle of the photophase, 25 individual were frozen when they had reached both the L2 and the L4 stages, in the two photoperiodic conditions. Thus, 25 individuals from 4 different stages (L4-G0, WA-G0, L2-G1 and L4-G1) were collected in the two photoperiod conditions with 3 biological replicates, forming the 24 samples used for microarray experiments. RNAs from heads of aphids from the two photoperiodic conditions were hybridized one against the other for each stage with a dye-swap.The experimental design is thus 24 arrays which corresponds to the described samples of that series.
2010-06-19 | E-GEOD-15776 | biostudies-arrayexpress
Project description:We investigated the transcriptomic response to territorial intrusion in four regions of the brain (telencephalon, diencephalon, cerebellum and brain stem) of a teleost fish, the threespined stickleback (Gasterosteus aculeatus). We tested the hypothesis that gene regulatory networks modulate the transcriptional response to territorial intrusion in the different brain regions and thereby aggressive behavior. Indeed, transcription regulatory network analysis identified cis-regulatory transcription factor motifs enriched in upregulated genes in one brain region and downregulated in the others. We further validated our findings by showing that many of the differentially expressed genes in the diencephalon were positively correlated with levels of aggression in individual males. 2 conditions: control fish and fish that experienced intrusion into their territory, Biological replicates 5.Four brain regions. Sample 4BS was excluded from the analysis during data preprocessing because it was an outlier.
2012-11-21 | E-GEOD-32961 | biostudies-arrayexpress