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Small non-coding RNA expression profile in F1 progeny from irradiated adults zebrafish

ABSTRACT: small non-coding RNA expression profile in F1 progeny from irradiated adults zebrafish

PROVIDER: PRJNA638603 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11974578.fastq.gz	Fastqsanger.gz
	SRR11974579.fastq.gz	Fastqsanger.gz
	SRR11974580.fastq.gz	Fastqsanger.gz
	SRR11974581.fastq.gz	Fastqsanger.gz
	SRR11974582.fastq.gz	Fastqsanger.gz

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small non-coding RNA expression profile in F1 progeny from irradiated adults zebrafish

Project description:In order to investigate transcriptomic mechanisms underlying radiation exposure, we exposed zebrafish (~6 month old) to 8.7 mGy/h of g-radiation (5.2 Gy total dose) during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at 5.5 hpf (late blastula/early gastrula) one year after parental exposure, for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed (F1-γ), and control (F1-C) parents, revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall, 22 miRNAs, 11 piRNA clusters, 19 snRNAs, and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data, a total of 672 differentially expressed mRNAs could be linked to the DEmiRs, of which 380 followed the canonical inverse relation in miRNA-mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor, NFkB and PTEN signaling, linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down-regulated in the F1-γ group, 68.8% of which were U1 and U2 snRNAs. In addition, 45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs (LTR, LINE, and TIR) (p=0.0024). DEpiRNA clusters were expressed from the opposite strand of the associated TEs, indicating expression of DEpiRNAs in response to activation of TEs. Finally, 66.7% and 33.3% of lincRNAs in F1-γ were down- and up-regulated respectively. The cancer and development related lincRNAs malat-1 was found among the most down-regulated genes, denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies.

2021-02-09 | GSE152189 | GEO

AKHR F1 heterozygous progeny of obese parents and controls, 10-11 days old adults

Project description:Transgenerational effects of parental metabolic state have been shown, but the mechanism is still unclear. Here we present transcriptome sequencing data from AKHR heterozygous F1 progeny, either from obese maternal or paternal parents, compared to genetically matched heterozygous controls or to wild-type controls

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Gene copy analysis of the F1 haploid progeny generated by Hypocrea jecorina CBS999.9 sexual development

Project description:H. jecorina undergoes a heterothallic reproductive cycle, and the mating yields asci with 16 linearly arranged ascospores. The sixteen ascospores are generated via two rounds of postmeiotic mitosis following the two meiotic divisions. We have discovered that viable aneuploid ascosporesare are frequently (~90%) generated due to a net gain of a conserved ~500 kbp genomic segment. Here we have compared whole genome gene copy number changes in the aneuploid F1 progeny, euploid F1 progeny, parental strains and the F1 progeny of RTU strain backcross with CBS999.97 .

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Gene copy analysis of the F1 haploid progeny generated by Hypocrea jecorina CBS999.9 sexual development

2015-01-07 | E-GEOD-41965 | biostudies-arrayexpress

Gene copy analysis of the F1 haploid progeny generated by Hypocrea jecorina CBS999.97 sexual development

Project description:Array-based comparative genome hybridization. H. jecorina undergoes a heterothallic reproductive cycle, and the mating yields asci with 16 linearly arranged ascospores. Here we have compared whole genome gene copy number in the F1 progeny.

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Genomic DNA copy number aberration in chromosome 18 of small intestinal tumors in B6/B6-Chr18MSM-F1 ApcMin/+ mice irradiated with ionizing radiation

Project description:To investigate DNA copy number changes in chromosome 18 of small intestinal tumors in B6/B6-Chr18MSM-F1 ApcMin/+ mice irradiated with ionizing radiation

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RNAseq of human neutrophil small non-coding RNAs from adults with SLE and age-matched healthy controls

Project description:We report small non-coding RNA expression in blood neutrophils from (1) healthy adults (2) adults with systemic lupus erythematosus (SLE).

2026-07-16 | GSE318027 | GEO

Vitis vinifera cultivar:Red Globe x Crimson Seedless F1 progeny

Project description:Vitis vinifera cultivar:Red Globe x Crimson Seedless F1 progeny Transcriptome or Gene expression

| PRJNA307074 | ENA

Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish (Danio rerio) progeny

Project description:Disproportionate high intake of n-6 polyunsaturated fatty acids (PUFAs) in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n-6 PUFA arachidonic acid (ARA) in the parental diet. The parental generation (F0) was fed a diet which was either low (control) or high in ARA (high ARA). Progenies of both groups (F1) were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless, several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long-chain fatty acid metabolism. The enrichment of genes involved in β-oxidation observed in the progeny, corresponded to the increase in peroxisomal β-oxidative degradation of long-chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition, estrogen signalling was found to be affected by parental high dietary ARA levels, where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n-3/n-6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated.

2018-10-06 | GSE104692 | GEO

Taurine ameliorates oxidative stress of BMSCs and promotes osteogenesis in irradiated jaws

Project description:Osteoradionecrosis of the jaw (ORNJ) is a complication after head and neck radiotherapy that severely affects patients’ quality of life. Currently, an overall understanding of microenvironmental factors of ORNJ is still lacking. Here, we reveal the activation of taurine metabolism in irradiated mandibular stromal cells with scRNA-Seq and the decrease of taurine in irradiated bone marrow mesenchymal stromal cells (BMSCs) with metabolomics. Compared to the unirradiated BMSCs, the taurine uptake of irradiated BMSCs increases. The taurine concentration in peripheral blood and jaws of irradiated mice are significantly lower than the unirradiated mice. Supplementation of taurine promotes osteogenic differentiation, decreases oxidative stress and DNA damage of irradiated BMSCs. Oral administration of taurine significantly promotes survival rate of irradiated mice and promotes osteogenesis of irradiated jaws. Our study sheds light on the role of taurine during the recovery of radiation-induced jaw injury, suggesting a potential non-invasive therapeutic means to combat ORNJ.

2024-07-08 | MTBLS10284 | MetaboLights

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