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Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish II.

ABSTRACT: To explore the effects of the housing condition (group- or single-housing) on killifish, we performed RNA-seq analysis for the whole bodies of male and female juveniles, gonads of males and females from puberty to middle age, and livers of young and old males.

ORGANISM(S): Nothobranchius furzeri

PROVIDER: GSE245481 | GEO | 2024/10/13

REPOSITORIES: GEO

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Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish I.

Project description:To explore the effects of the housing condition (group- or single-housing) on killifish, we performed RNA-seq analysis for the whole bodies of male and female juveniles, gonads of males and females from puberty to middle age, and livers of young and old males.

2024-10-13 | GSE245480 | GEO

Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish

Project description:Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish

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Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish II.

Project description:Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish II.

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Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish I.

Project description:Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish I.

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Circular RNAs in the ageing African turquoise killifish

Project description:In this work we took 9 samples from brain and 6 samples from muscle of the African turquoise killifish (Nothobranchius furzeri) at 3.5, 8.5 and 14 weeks. Total RNA was sequenced and circRNAs were detected.

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Effect of housing condition (group- or single-housing) on gene expression in African turquoise killifish

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-10-13 | GSE245483 | GEO

Circular RNAs in the ageing African turquoise killifish

Project description:Circular RNAs in the ageing African turquoise killifish

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Chromosome conformation capture (Hi-C) of the turquoise killifish

Project description:This approach was used to increase the continuity of the killifish genome, and assess the relative distance of specific genes from the sex locus.

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Project description:Age-related vision loss caused by retinal neurodegenerative pathologies is becoming more prevalent in our ageing society. To understand the physiological and molecular impact of ageing on retinal homeostasis, we used the short-lived African turquoise killifish, a model known to naturally develop central nervous system (CNS) ageing hallmarks and vision loss. Bulk and single-cell RNA-sequencing (scRNAseq) of three age groups (6-, 12-, and 18-week-old) identified transcriptional ageing fingerprints in the killifish retina, unveiling pathways also identified in the aged brain, including oxidative stress, gliosis, and inflammageing. These findings were comparable to observations in the ageing mouse retina. Additionally, transcriptional changes in genes related to retinal diseases, such as glaucoma and age-related macular degeneration, were observed. The cellular heterogeneity in the killifish retina was characterized, confirming the presence of all typical vertebrate retinal cell types. Data integration from age-matched samples between the bulk and scRNAseq experiments revealed a loss of cellular specificity in gene expression upon ageing, suggesting potential disruption in transcriptional homeostasis. Differential expression analysis within the identified cell types highlighted the role of glial/immune cells as important stress regulators during ageing. Our work emphasizes the value of the fast-ageing killifish in elucidating molecular signatures in age-associated retinal disease and vision decline. This study contributes to the understanding of how age-related changes in molecular pathways may impact CNS health, providing insights that may inform future therapeutic strategies for age-related pathologies.

| S-EPMC11320354 | biostudies-literature

Project description:Age-related vision loss caused by retinal neurodegenerative pathologies is becoming more prevalent in our ageing society. To understand the physiological and molecular impact of ageing on retinal homeostasis, we used the short-lived African turquoise killifish, a model known to naturally develop central nervous system (CNS) ageing hallmarks and vision loss. Bulk and single-cell RNA-sequencing (scRNA-seq) of three age groups (6-, 12-, and 18-week-old) identified transcriptional ageing fingerprints in the killifish retina, unveiling pathways also identified in the aged brain, including oxidative stress, gliosis, and inflammageing. These findings were comparable to observations in ageing mouse retina. Additionally, transcriptional changes in genes related to retinal diseases, such as glaucoma and age-related macular degeneration, were observed. The cellular heterogeneity in the killifish retina was characterised, confirming the presence of all typical vertebrate retinal cell types. Data integration from age-matched samples between the bulk and scRNA-seq experiments revealed a loss of cellular specificity in gene expression upon ageing, suggesting potential disruption in transcriptional homeostasis. Differential expression analysis within the identified cell types highlighted the role of glial/immune cells as important stress regulators during ageing. Our work emphasises the value of the fast-ageing killifish in elucidating molecular signatures in age-associated retinal disease and vision decline. This study contributes to the understanding of how age-related changes in molecular pathways may impact CNS health, providing insights that may inform future therapeutic strategies for age-related pathologies.

| S-EPMC10979842 | biostudies-literature

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