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Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster [WGBS]

ABSTRACT: Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster [WGBS]

PROVIDER: PRJNA821535 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18548541_1.fastq.gz	Fastqsanger.gz
	SRR18548541_2.fastq.gz	Fastqsanger.gz
	SRR18548542_1.fastq.gz	Fastqsanger.gz
	SRR18548542_2.fastq.gz	Fastqsanger.gz
	SRR18548543_1.fastq.gz	Fastqsanger.gz

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Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster [WGBS]

Project description:Hibernation consist of alternating torpor/arousal phases, during which animals cope with repetitive hypothermia and ischemia-reperfusion. Due to limited transcriptomic and methylomic information for facultative hibernators, we here conducted RNA and whole genome bisulfite sequencing in liver of hibernating Syrian hamster (Mesocricetus auratus). Gene Ontology analysis was performed on 844 differentially expressed genes (DEGs) and confirmed the shift in metabolic fuel utilization, inhibition of RNA transcription and cell cycle regulation as found in seasonal hibernators. We show a so far unreported suppression of MAPK and PP1 pathways. Notably, hibernating hamsters showed upregulation of MAPK inhibitors (DUSPs and SPRYs) and reduced levels of MAPK induced transcription factors. Promoter methylation was found to modulate the expression of genes targeted by these transcription factors. In conclusion, we document gene regulation between hibernation phases, which may aid the identification of pathways and targets to prevent organ damage in transplantation or ischemia-reperfusion.

2023-05-02 | GSE199815 | GEO

Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster [RNA-Seq]

Project description:Hibernation consist of alternating torpor/arousal phases, during which animals cope with repetitive hypothermia and ischemia-reperfusion. Due to limited transcriptomic and methylomic information for facultative hibernators, we here conducted RNA and whole genome bisulfite sequencing in liver of hibernating Syrian hamster (Mesocricetus auratus). Gene Ontology analysis was performed on 844 differentially expressed genes (DEGs) and confirmed the Liver, shift in metabolic fuel utilization, inhibition of RNA transcription and cell cycle regulation as found in seasonal hibernators. We Liver, show a so far unreported suppression of MAPK and PP1 pathways. Notably, hibernating hamsters Liver, showed upregulation of MAPK inhibitors (DUSPs and SPRYs) and reduced levels of MAPK induced transcription factors. Promoter methylation was found to modulate the expression of genes targeted by these transcription factors. In conclusion, we document gene regulation between hibernation phases, which may aid the identification of pathways and targets to prevent organ damage in transplantation or ischemia-reperfusion.

2023-05-02 | GSE199814 | GEO

Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster

Project description:Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster

| PRJNA821531 | ENA

Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster [RNA-Seq]

Project description:Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster [RNA-Seq]

| PRJNA821536 | ENA

Transcriptional profiling of Control vs. Pinealectomised Syrian hamster testes

Project description:Transcriptional profiling of male Syrian hamster testes, comparing control animals with those that have had a pinealectomy. Keywords: transcriptional profiling Two-condition experiment, Control vs pinealectomised animals

2010-05-26 | E-GEOD-10078 | biostudies-arrayexpress

Transcriptional profiling of Control vs. Pinealectomised Syrian hamster testes

Project description:Transcriptional profiling of male Syrian hamster testes, comparing control animals with those that have had a pinealectomy. Keywords: transcriptional profiling

2008-01-08 | GSE10078 | GEO

Liver transcriptomic and methylomic analyses identify transcriptional MAPK regulation in facultative hibernation of Syrian hamster

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

2023-05-02 | GSE199817 | GEO

RNA-Seq of hamster PDAC cancer (HapT1 cell line) biopsies taken after treatment with either an IgG control or new hamster specific anti-PD-L1 monoclonal antibody.

Project description:1. The experiment was performed to assess if the newly discovered Syrian hamster specific anti-PD-L1 antibody could induce a biologically relevant change in transcriptome profile in the tumours. This would confirm that the antibody has functional properties. In the larger picture, the Syrian Hamster model is favored over the mouse model for the development of vaccines and testing of oncolytic viruses/immunotherapies. This is because the model is semi permissive to virus replication compared to the mouse model. We can therefore more reliably assess the efficacy of oncolytic virotherapies, mainly oncolysis and promoter specific transgene expression. Moreover, we wanted to test potential improvements to treatment outcomes when combining oncolytic virotherapy and immune checkpoint blockade. However, there are not many commercially available research tools specific to the Syrian Hamster. This is why we developed an in vivo compatible immune checkpoint inhibitor so that we could assess the combination therapy in the Syrian hamster model. Lastly, we also wanted to validate if we could assess the efficacy of the immunotherapies using biopsies from hamsters to remove unnecessary use of animals. 2. To do this, we engrafted one PDAC tumours on the right flank of Syrian hamsters using 5 x10E+6 HapT1 cells grown in culture. When tumours reached 4-5mm in diameter, the hamsters were injected intraperitoneally with either 300ug of IgG2a control or anti-PD-L1 (clone;11B12-1). Hamsters were treated 8 times and a tumour biopsy was taken one day before the last treatment. The biopsy was immediately stored in RNA-later until extraction with RNA mini kit (Qiagen).

2023-01-30 | E-MTAB-12297 | biostudies-arrayexpress

DNA methylation in Syrian hamster female fetal cells (gestation day 13.5) exposed in vitro to 5-aza-2’deoxycytidine (5aCdR)

Project description:Purpose: To validate the reduced representation bisulfite sequencing (RRBS) methodology by comparing DNA methylation pattern in Syrian hamster fetal (SHF) primary cells to a SHF cell line (MT2) exposed to the DNA methyl transferase inhibitor,5aCdR. The MT2 cell line was originally derived from the expansion of a benzo[a]pyrene-induced morphologically transformed clone (Pickles et al 2016. Mutat.Res.Genet.Toxicol.Environ Mutagen. 802:50-58).

2023-02-10 | GSE144797 | GEO

Changes in the gene expression in the inferior colliculus of the sound stimulated both control Syrian hamsters and the strain GASH:Sal.

Project description:Using microarray analyses and subsequent verification by RT-PCR, we studied the changes in gene expression in the inferior colliculus after an ictal event in one models of audiogenic epilepsy, genetic audiogenic seizure hamster (GASH:Sal). GASH:Sal, a hamster strain developed at the University of Salamanca, exhibits genetic audiogenic epilepsy similar to human Grand Mal epilepsy. GASH:Sal shows an autosomal recessive inheritance for susceptibility to audiogenic seizures, which manifest more severely in young animals; the seizure severity progressively declines with age. Genetic animal models of epilepsy are an important tool for further understanding the basic cellular mechanisms underlying epileptogenesis and for developing novel antiepileptic drugs. We conducted a comparative study of gene expression in the inferior colliculus, a nucleus that triggers audiogenic seizures, using two animal models, the Wistar audiogenic rat (WAR) and the genetic audiogenic seizure hamster (GASH:Sal). For this purpose, both models were subjected to auditory stimulation, and 60 minutes after stimulation, the inferior colliculi were collected. As a control, intact Wistar rats and Syrian hamsters were subjected to identical stimulation and tissue preparation protocols to those performed on the experimental animals. A total of 24 animals were used in this study according to the following distribution: 12 control Syrian hamsters (Mesocricetus auratus) and 12 GASH:Sal at 16 weeks of age and a body weight of approximately 60 g. Six animals Syrian and GASH:Sal hamsters, respectively, were exposed to auditory stimulation, and 60 min after the seizures, we harvested the IC for all gene expression analyses (stimulated Syrian hamsters and stimulated GASH:Sal hamsters). As controls, other six animals Syrian and GASH:Sal hamsters, respectively, were not exposed to the same stimulation (Syrian hamsters and GASH:Sal hamsters).

2015-12-31 | E-GEOD-74043 | biostudies-arrayexpress

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