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Genomic-Wide Transcriptomic Analysis of the Forebrain of postnatal Slc13a4+/- mice

ABSTRACT: Genomic-Wide Transcriptomic Analysis of the Forebrain of postnatal Slc13a4+/- mice

PROVIDER: PRJNA720843 | ENA |

REPOSITORIES: ENA

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Genomic-Wide Transcriptomic Analysis of the Forebrain of postnatal Slc13a4+/- mice

Project description:We performed bulk RNA-seq on Nas2Del +/- Het and wild type postnatal Day 20 mice on samples collected from the mouse forebrain.

2021-04-10 | GSE171765 | GEO

Genome-wide transcriptomic analysis of the forebrain of postnatal Slc13a4<sup>+/-</sup> mice.

Project description:ObjectiveSulfation is an essential physiological process that regulates the function of a wide array of molecules involved in brain development. We have previously shown expression levels for the sulfate transporter Slc13a4 to be elevated during postnatal development, and that sulfate accumulation in the brains of Slc13a4+/- mice is reduced, suggesting a role for this transporter during this critical window of brain development. In order to understand the pathways regulated by cellular sulfation within the brain, we performed a bulk RNA-sequencing analysis of the forebrain of postnatal day 20 (P20) Slc13a4 heterozygous mice and wild-type litter mate controls.Data descriptionWe performed an RNA transcriptomic based sequencing screen on the whole forebrain from Slc13a4+/- and Slc13a4+/+mice at P20. Differential expression analysis revealed 90 differentially regulated genes in the forebrain of Slc13a4+/- mice (a p-value of 0.1 was considered as significant). Of these, 55 were upregulated, and 35 were downregulated in the forebrain of heterozygous mice. Moreover, when we stratified further with a ± 1.2 fold-change, we observed 38 upregulated, and 16 downregulated genes in the forebrain of heterozygous mice. This resource provides a useful tool to interrogate which pathways may require elevated sulfate levels to drive normal postnatal development of the brain.

| S-EPMC8276513 | biostudies-literature

Genomic Resolution of DLX-orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons

Project description:DLX transcription factors (TFs) are master regulators of the developing vertebrate brain, driving forebrain GABAergic neuronal differentiation. Ablation of Dlx1&2 alters expression of genes that are critical for forebrain GABAergic development. We integrated epigenomic and transcriptomic analyses, complemented with in situ hybridization (ISH), and in vivo and in vitro studies of regulatory element (RE) function. This elucidated the DLX-organized gene regulatory network at genomic, cellular, and spatial level in mouse embryonic basal ganglia. DLX TFs perform dual activating and repressing functions; the consequences of their binding were determined by the sequence and genomic context of target loci. Our results reveal and, in part, explain the paradox of widespread DLX binding contrasted with a limited subset of target loci that are sensitive at the epigenomic and transcriptomic level to Dlx1&2 ablation. The regulatory properties identified here for DLX TFs suggest general mechanisms by which TFs orchestrate dynamic expression programs underlying neurodevelopment.

2019-08-20 | GSE124936 | GEO

WGBS from forebrain (ENCSR020GGM)

Project description:Whole genome bisulfite-seq on postnatal 0 day mouse forebrain For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf https://www.encodeproject.org/ENCSR020GGM/

2016-06-22 | E-GEOD-82356 | biostudies-arrayexpress

mRNAseq in forebrain and cerebellum of wild-type mice at postnatal 2 weeks age

Project description:We sequenced mRNA from mouse brain to compare gene expression level between 2 forebrain and 2 cerebellum.

2022-12-29 | GSE221867 | GEO

WGBS from forebrain (ENCSR020GGM)

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microRNA-seq from forebrain (ENCSR267CQC)

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2016-06-22 | E-GEOD-82558 | biostudies-arrayexpress

ChIP-seq from forebrain (ENCSR070MOK)

Project description:H3K27me3 ChIP-seq on postnatal 0 day mouse forebrain For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf https://www.encodeproject.org/ENCSR070MOK/

2016-06-22 | E-GEOD-82404 | biostudies-arrayexpress

ChIP-seq from forebrain (ENCSR069TDC)

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ChIP-seq from forebrain (ENCSR093DWU)

Project description:H3K9me3 ChIP-seq on postnatal 0 day mouse forebrain For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf https://www.encodeproject.org/ENCSR093DWU/

2016-06-22 | E-GEOD-82425 | biostudies-arrayexpress

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