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| Status |
Public on May 06, 2019 |
| Title |
Effects of gene-by-environment interaction on the transcriptome of mice deficient for tryptophan hydroxylase 2 [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
RNA expression profiles affected by maternal separation, brain 5-HT deficiency and their interaction in adult male mice, were generated using RNA deep sequencing
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| Contributor(s) |
Lesch KP, van den Hove D, Weidner MT, Förrstner KU, Eijsen L, Lardenoije R |
| Citation(s) |
31133792 |
| Submission date |
Feb 08, 2018 |
| Last update date |
Aug 20, 2019 |
| Contact name |
Konrad U. Förstner |
| E-mail(s) |
foerstner@zbmed.de
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| Organization name |
ZB MED - Information Centre for Life Sciences
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| Department |
Information Services
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| Lab |
Förstner Lab
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| Street address |
Gleueler Str. 60
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| City |
Cologne |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
50931 |
| Country |
Germany |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (48)
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| This SubSeries is part of SuperSeries: |
| GSE110330 |
Effects of gene-by-environment interaction on the transcriptome and methylome of mice deficient for tryptophan hydroxylase 2 |
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| Relations |
| BioProject |
PRJNA433807 |
| SRA |
SRP132678 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE110328_Gene-wise_read_countings.txt.gz |
1000.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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