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Mus musculus strain:C57BL/6J

ABSTRACT: FMRP RIP-seq using CNS tissues of E14.5 mouse embryos

PROVIDER: PRJDB7973 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR168489.fastq.gz	Fastqsanger.gz
	DRR168490.fastq.gz	Fastqsanger.gz
	DRR168491.fastq.gz	Fastqsanger.gz
	DRR168492.fastq.gz	Fastqsanger.gz
	DRR168493.fastq.gz	Fastqsanger.gz

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Mus musculus strain:C57BL/6J

Project description:RNA-seq using telencephalons of mouse embryos

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Unstranded RNA-seq profiling of cerebral cortices from Taf8-deleted and Taf8-intact mouse embryos

Project description:Taf8 was deleted in the mouse central nervous system using our Taf8 conditional allele. To determine transcriptional changes due to Ta8 deletion in the developing CNS, unstranded RNA sequencing was performed on cortices from Taf8 deleted embryos (E14.5 Taf8lox/–NesCreT/+p53–/–) and control embryos (E14.5 Taf8+/+NesCreT/+p53–/–).

2022-03-12 | GSE198503 | GEO

Stranded RNA-seq profiling of cerebral cortices from Taf8-deleted and Taf8-intact mouse embryos

Project description:Taf8 was deleted in the mouse central nervous system using our Taf8 conditional allele. To determine transcriptional changes due to Ta8 deletion in the developing CNS, stranded RNA sequencing was performed on cortices from Taf8 deleted embryos (E14.5 Taf8lox/–NesCreT/+p53–/–) and control embryos (E14.5 Taf8+/+NesCreT/+p53–/–).

2022-03-12 | GSE198502 | GEO

Transcriptomic analyses of gastrulation-stage C57BL/6J and C57BL/6NHsd mouse embryos with differential susceptibility to alcohol

Project description:Craniofacial and CNS malformations characteristic of Fetal Alcohol Syndrome are caused by alcohol exposure during gastrulation (embryonic day [E]7 in mice; 2nd – 3rd week of human pregnancy). Genetics are a known contributor to differences in alcohol sensitivity in humans, and between different animal model strains such as C57BL/6J and C57BL/6NHsd mice. To investigate how these two genetically similar mouse strains differ in alcohol sensitivity, we profiled gene expression at baseline (E7.0) and 6 or 12 hours after alcohol exposure (E7.25–E7.5) in gastrulation-stage embryos. Many of the baseline transcriptional differences across strains were associated with immune signaling, indicative of their molecular divergence. Alcohol exposure was associated with a more pronounced transcriptional effect in 6J than in 6N, matching the 6J’s increased sensitivity. Alcohol exposure upregulated pathways related to cell death, stress, and hypoxia, and downregulated proliferation and morphogenic pathways. Dysregulated genes were also associated with craniofacial and CNS defects, but only in the 6J embryos. These data demonstrate the genetic variation that can contribute to the effects of prenatal alcohol and identify impacted molecular pathways, including higher baseline expression of inflammatory signaling genes in 6J embryos that likely increases sensitivity to teratogens such as alcohol. Collectively, our data provide a valuable resource that not only enables the discovery of biomarkers pertinent to prenatal alcohol exposure, but also facilitates the transcriptional comparison of two genetically similar mouse strains at three finely resolved developmental timepoints. To this end, we developed a web-based interactive tool to aid in data exploration available at http://parnell-lab.med.unc.edu/Embryo-Transcriptomics/.

2021-06-01 | GSE163796 | GEO

BG4 RIP-seq using mouse forebrain tissues

Project description:BG4 RIP-seq using mouse forebrain tissues

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Murine embryonic lung development: time course (C57BL/6J)

Project description:We generated gene expression profiles of 5 time points in murine lung development (E11.5, E13.5, E14.5, E16.5 and P5). The goal of this study was to establish a reference data set for exploration of large-scale similarities between transcriptomes in development and cancer. Keywords: time course

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Project description:Mfsd7c is expressed in CNS blood vessels. Deletion of Mfsd7c results in embryonic lethality with signs of hypoxia. We performed transcriptomic analysis of genes in brains of E14.5 wild-type (WT) and Mfsd7c-knockout (KO) embryos.

2020-05-18 | GSE148854 | GEO

Mus musculus strain:C57BL/6J

Project description:hnRNP-A/B RIP-seq in olfactory sensory neurons

| PRJDB13514 | ENA

RNAseq analysis of two independent stains of C57BL/6J-Plat-/- mice and wild-type C57BL/6J.

Project description:The ability to generate defined null mutations in mice revolutionized the analysis of gene function in mammals. However, gene-deficient mice generated by using 129-derived embryonic stem (ES) cells may carry large segments of 129 DNA, even when extensively backcrossed to reference strains, such as C57BL/6J, and this may confound interpretation of experiments performed in these mice. Tissue plasminogen activator (tPA), encoded by the PLAT gene, is a fibrinolytic serine protease that is widely expressed in the brain. A large number of neurological abnormalities have been reported in tPA-deficient mice. The studies here compare genes differentially expressed in the brains of Plat-/- mice from two independent Plat-/- mouse derivations to wild-type C57BL/6J mice. One strain denoted “Old” was constructed in ES cells from a 129 mouse and backcrossed extensively to C57BL/6J, and one denoted “New” Plat-/- mouse was constructed using zinc finger nucleases directly in the C57BL/6J-Plat-/- mouse strain. We identify a significant set of genes that are differentially expressed in the brains of Old Plat-/- mice that preferentially cluster in the vicinity of Plat on chromosome 8, apparently linked to more than 20 Mbp of DNA flanking Plat being of 129 origin. No such clustering is seen in the New Plat-/- mice.

2016-12-16 | GSE76093 | GEO

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