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Effects of gene-by-environment interaction on the transcriptome and methylome of mice deficient for tryptophan hydroxylase 2

ABSTRACT: Effects of gene-by-environment interaction on the transcriptome and methylome of mice deficient for tryptophan hydroxylase 2

PROVIDER: PRJNA433806 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6706350_1.fastq.gz	Fastqsanger.gz
	SRR6706350_2.fastq.gz	Fastqsanger.gz
	SRR6706360_1.fastq.gz	Fastqsanger.gz
	SRR6706360_2.fastq.gz	Fastqsanger.gz
	SRR6706370_1.fastq.gz	Fastqsanger.gz

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Effects of gene-by-environment interaction on the methylome of mice deficient for tryptophan hydroxylase 2 [MBD-seq]

Project description:Effects of gene-by-environment interaction on the methylome of mice deficient for tryptophan hydroxylase 2 [MBD-seq]

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Effects of gene-by-environment interaction on the transcriptome of mice deficient for tryptophan hydroxylase 2 [RNA-seq]

Project description:Effects of gene-by-environment interaction on the transcriptome of mice deficient for tryptophan hydroxylase 2 [RNA-seq]

| PRJNA433807 | ENA

Effects of gene-by-environment interaction on the methylome of mice deficient for tryptophan hydroxylase 2 [MBD-seq]

Project description:Purpose: Investigation of effects of early adversity in mice deficient for brain serotonin on the methylome Methods: Following materal separation in early childhood and behavioural screening in adulthood, 4 moth old males, either wildtype or carrying a hetero- or homozygous knockout of the thryptophan hyroxylase 2 gene, were sacrificed, brains extracted, the amygdalae of both hemispheres dissected, blended and separated in two protions. From one of these portions DNA was processed by an external company, i.e. Nxt-Dx (Ghent, Belgium). DNA was sheared by sonication, followed by methyl binding domain (MBD) based capture, leading to an enrichment of methylated fragments. Subsequently, library preparation was performed followed by multiplexed paired-end sequencing with a read-length of 50 bp and an approximate output of 20 million reads/sample on the Illumina HiSeq4000 platform. Reads were mapped to the Mus musculus GRCm38.p5 genome using Bowtie2 (v2.1.0) software in end-to-end & sensitive-mode. After mapping, coverage peaks were generated using MACS 14 peak caller (Zhang et al. 2008). Results: Either Tph2 genotype, early adversity as well as their interaction resulted in unique profiles of differentially enriched methylated peaks as well as expressed RNA. As expected, the effect sizes and significances were rather subtle and the overlap between top hits of methylome and transcriptome were marginal. Conclusion: Tph2, MS and their interaction induced changes in gene expression and DNA methylation, within a physiological range. The observed changes by MS seemed furthermore strongly influenced by the Tph2 genotype, ergo brain 5-HT availability.

2019-05-06 | GSE110329 | GEO

Effects of gene-by-environment interaction on the transcriptome and methylome of mice deficient for tryptophan hydroxylase 2

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

2019-05-06 | GSE110330 | GEO

Effects of gene-by-environment interaction on the transcriptome of mice deficient for tryptophan hydroxylase 2 [RNA-seq]

Project description:Purpose: Investigation of effects of early adversity in mice deficient for brain serotonin on the transcriptome Methods: Following materal separation in early childhood and behavioural screening in adulthood, 4 moth old males, either wildtype or carrying a hetero- or homozygous knockout of the thryptophan hyroxylase 2 gene, were sacrificed, brains extracted, the amygdalae of both hemispheres dissected, blended and separated in two protions. From one of these portions RNA was extracted. Extracted RNA was further processed by an external company, i.e. IGA Technologies (Udine, Italy). , library preparation was performed using TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, US) that captures coding RNA and multiple forms of non-coding RNA, with a total input of 300 ng of RNA, as measured with Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) following manufacturer’s recommendations. The sequencing was performed using the Illumina HiSeq 2500 platform at a read-length of 125 bp with paired end reads yielding 60 million reads/sample. Reads were mapped to the Mus musculus GRCm38.p5 genome using STAR (Dobin et al. 2013). Following mapping, the reads per position were determined using HTSeq (Anders et al. 2015). Results: Either Tph2 genotype, early adversity as well as their interaction resulted in unique profiles of differentially expressed RNA. As expected, the effect sizes and significances were rather subtle. Conclusion: Tph2, MS and their interaction induced changes in gene expression and DNA methylation, within a physiological range. The observed changes by MS seemed furthermore strongly influenced by the Tph2 genotype, ergo brain 5-HT availability.

2019-05-06 | GSE110328 | GEO

N-hydroxylase

Project description:N-hydroxylase

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Interleukin-33 induces the enzyme tryptophan hydroxylase 1 to promote inflammatory group 2 innate lymphoid cell-mediated immunity

Project description:Interleukin-33 induces the enzyme tryptophan hydroxylase 1 to promote inflammatory group 2 innate lymphoid cell-mediated immunity

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Post-epidemic eosinophilia myalgia syndrome associated with L-Tryptophan

Project description:Eosinophilia–myalgia syndrome (EMS) is characterized by subacute onset of myalgias and peripheral eosinophilia, followed by chronic neuropathy and skin induration. The EMS epidemic in 1989 was linked to L-tryptophan consumption originating from a single source. Following the Food and Drug Administration (FDA) ban on the sale of L-tryptophan, the incidence of EMS declined rapidly. Moreover, no new cases have been published since the FDA ban was lifted in 2005. We report the clinical, histopathological and immunogenetic features of a new case of L-tryptophan-associated EMS along with evidence of activated transforming growth factor-ß and interleukin-4 signaling in the lesional skin. 6 samples were analyzed to include EMS patient and two replicates along with three normal controls

2012-01-28 | E-GEOD-26934 | biostudies-arrayexpress

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Tryptophan metabolism response in E. coli

Project description:DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. We investigated the global changes in mRNA abundance in Escherichia coli elicited by various perturbations of tryptophan metabolism. To do so we printed DNA microarrays containing 95% of all annotated E. coli ORFs. We determined the expression profile that is predominantly dictated by the activity of the tryptophan repressor. Only three operons, trp, mtr, and aroH, exhibited appreciable expression changes consistent with this profile. The quantitative changes we observed in mRNA levels for the five genes of the trp operon were consistent within a factor of 2, with expectations based on established Trp protein levels. Several operons known to be regulated by the TyrR protein, aroF-tyrA, aroL, aroP, and aroG, were down-regulated on addition of tryptophan. TyrR can be activated by any one of the three aromatic amino acids. Only one operon, tnaAB, was significantly activated by the presence of tryptophan in the medium. We uncovered a plethora of likely indirect effects of changes in tryptophan metabolism on intracellular mRNA pools, most prominent of which was the sensitivity of arginine biosynthetic operons to tryptophan starvation. This study is detailed in Khodursky AB et al.(2000) Proc Natl Acad Sci U S A 97:12170-5 Keywords: other

2001-07-30 | GSE7 | GEO

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