EpiFishGrowth Work Package 1 Muscle - RNA-Seq (raw, unaligned)

10.1017/S0007114521002336

Muscle samples of Atlantic salmon fed two different micronutrient packages were collected at pre-smolt and post-smolt stages for RNA-seq.

NutrEpi Work Package 1 Gonad - RNA-Seq (raw, unaligned)

10.1080/15592294.2020.1859867

Three groups of Atlantic salmon were fed with graded levels of micronutrient package. 18 male gonad samples were collected at the final harvest stage for RNA-seq.

Salmo salar Transcriptome

10.3389/fgene.2021.656334

Salmo salar transcriptome resource using PacBio SMRT sequencing and Illumina short-read sequencing on multiple physiological conditions and tissue types.

Bulk RNA-seq of mice covering the whole lifespan (2 days to 904 days) from four tissues

Gene expression changes during ageing were shown to oppose developmental trajectories; a reversal pattern previously linked to cellular identity loss. Generating cortex, lung, liver and muscle tissue transcriptomes of 16 mice of different ages, covering development and ageing periods, we found that expression reversals were widespread but tissue-specific. Consistent with this result, we observed an inter-tissue divergence during development and convergence during ageing (DiCo), further confirmed in independent mouse and human datasets. The genes displaying DiCo pattern were enriched among tissue-specific genes that tended to lose developmental expression levels during ageing. Finally, analysing publicly available single-cell transcriptome data, we studied the contribution of cellular composition and cell-autonomous changes to the convergence in ageing. Our results, for the first time, suggest inter-tissue convergence during ageing is widespread and associated with the loss of specialisation at the tissue and possibly also at the cellular level. Overall design: Age-series mRNA expression profiles from 4 tissues (cerebral cortex, lung, liver, skeletal muscle) of 16 mice, covering postnatal development (2 days - 61 days) and ageing (93 days - 904 days) periods.

Flesh coloration on Atlantic salmon

We compared Illumina TruSeq kit, the standard RNA-Seq and Lexogen QuantSeq kit, the 3 mRNA-Seq method for an Atlantic salmon flesh color investigation. Firstly, QuantSeq was used to compare differentially expressed genes between four different flesh color phenotypes. To confirm the results and to analyze whether there are any differences between TruSeq and QuantSeq, TruSeq was used on two chosen sample subsets from two flesh color phenotypes.

Salmo salar testis microRNA

10.1186/s12864-017-4205-5

microRNA Salmo salar immature, pre-pubertal and pubertal testis

Defining early changes in Alzheimer's disease from RNA sequencing of brain regions deferentially affected by pathology

Tau pathology in Alzheimer's disease (AD) spreads in a predictable pattern that corresponds with disease symptoms and severity. At post-mortem there are cortical regions that range from mildly to severely affected by tau pathology and neuronal loss. A comparison of the molecular signatures of these differentially affected areas within cases and between cases and controls may allow the temporal modelling of disease progression. Here we used RNA sequencing to explore differential gene expression in the mildly affected primary visual cortex and moderately affected precuneus of ten age-, gender- and RNA quality-matched post-mortem brains from AD patients and healthy controls. The two regions in AD cases had similar transcriptomic signatures but there were broader abnormalities in the precuneus consistent with the greater tau load. Both regions were characterised by upregulation of immune-related genes such as those encoding triggering receptor expressed on myeloid cells 2 and membrane spanning 4-domains A6A and milder changes in insulin/IGF1 signalling. The precuneus in AD was also characterised by changes in vesicle secretion and downregulation of the interneuronal subtype marker, somatostatin. The 'early' AD transcriptome is characterised by perturbations in synaptic vesicle secretion on a background of neuroimmune dysfunction. In particular, the synaptic deficits that characterise AD may begin with the somatostatin division of inhibitory neurotransmission.

Social boldness correlates with brain gene expression in male green anoles

Our study focuses on constitutive gene expression in bold and shy individuals by isolating baseline gene expression profiles that influence social boldness predisposition, rather than those reflecting the results of social interaction and behavioral execution. We performed this study on male green anole lizards (Anolis carolinensis), an established model organism for behavioral research, which provides a crucial comparison group to investigations of birds and mammals.

Effects of yeast species and processing on transcriptomic profile and intestinal health of Atlantic salmon (Salmo salar) fed soybean meal-based diets in seawater

10.3390/ijms23031675

The objective of the current study was to examine the effects of yeasts on intestinal health and transcriptomic profile of Atlantic salmon fed SBM-based diets in seawater. Cyberlindnera jadinii (CJ) and Wickerhamomyces anomalus (WA) yeasts were produced in-house and processed by direct heat-inactivation with spray-drying (ICJ and IWA) or autolyzed at 50 ºC for 16 h (ACJ and AWA), followed by spray-drying. Six diets were formulated, one based on fishmeal (FM), a challenging diet with 30% soybean meal (SBM) and four other diets containing 30% SBM and 10% of each of the four yeast fractions (i.e., ICJ, ACJ, IWA and AWA). The results showed that the inclusion of CJ yeasts reduced loss of supranuclear vacuolization, along with reduction in population of CD8α positive cells present in the lamina propria of fish fed the SBM diet. The CJ yeasts controlled the inflammatory profile of fish fed SBM through up-regulation of pathways related to wound healing and taurine metabolism. Additionally, the WA yeasts dampened the inflammatory profile of fish fed SBM through down-regulation of pathways related to toll-like receptor signaling, C-lectin receptor, cytokine receptor and signal transduction. The results suggest that yeasts could be used as protein ingredients with functional properties in diets for Atlantic salmon. Overall design: Examination of intestinal health of Atlantic salmon fed diets containing four different yeast treatments.

Long-term performance of gene edited, sterile Atlantic salmon (RNA seq)

In this study, germ cell-free (dnd-knockout) and wild type Atlantic salmon were reared common garden under standard commercial conditions throughout a production cycle and then harvested. Fish performance in terms of growth, welfare indictors, gene expression in non-target tissues and fillet quality were evaluated.

Cell Type- and Tissue-specific Enhancers in Craniofacial Development [human RNA]

The genetic basis of craniofacial birth defects and general variation in human facial shape remains poorly understood. Distant-acting transcriptional enhancers are a major category of non-coding genome function and have been shown to control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic location and cell type-specific in vivo activities of all craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combined transcriptome, histone modification, and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution. In total, we identified approximately 14,000 enhancers across seven developmental stages from weeks 4 through 8 of human embryonic face development. To annotate the cell type specificity of human-mouse conserved enhancers, we performed single-cell RNA-seq and single-nucleus ATAC-seq of mouse craniofacial tissues from embryonic days e11.5 to e15.5. By integrating across these data sets, we identify major cell populations of the developing face and annotate over 16,000 candidate enhancers by their cell type-specific epigenomic profile. Using retrospective analysis of known craniofacial enhancers in combination with single cell-resolved transgenic reporter assays, we show the value of these data for the prediction of in vivo cell type specificity. Taken together, our data provide a critical resource for genetic and developmental studies of human craniofacial development. Overall design: We combined transcriptome, histone modification, and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution.

Cell Type- and Tissue-specific Enhancers in Craniofacial Development [mouse RNA]

The genetic basis of craniofacial birth defects and general variation in human facial shape remains poorly understood. Distant-acting transcriptional enhancers are a major category of non-coding genome function and have been shown to control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic location and cell type-specific in vivo activities of all craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combined transcriptome, histone modification, and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution. In total, we identified approximately 14,000 enhancers across seven developmental stages from weeks 4 through 8 of human embryonic face development. To annotate the cell type specificity of human-mouse conserved enhancers, we performed single-cell RNA-seq and single-nucleus ATAC-seq of mouse craniofacial tissues from embryonic days e11.5 to e15.5. By integrating across these data sets, we identify major cell populations of the developing face and annotate over 16,000 candidate enhancers by their cell type-specific epigenomic profile. Using retrospective analysis of known craniofacial enhancers in combination with single cell-resolved transgenic reporter assays, we show the value of these data for the prediction of in vivo cell type specificity. Taken together, our data provide a critical resource for genetic and developmental studies of human craniofacial development. Overall design: We combined transcriptome, histone modification, and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution.

Danio rerio Raw sequence reads

normal RNAseq of zebrafish