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QuantSeq analysis in the hippocampus of WT and PHF2 t/g mice

ABSTRACT: QuantSeq analysis in the hippocampus of WT and PHF2 t/g mice

PROVIDER: PRJNA530240 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8832560.fastq.gz	Fastqsanger.gz
	SRR8832561.fastq.gz	Fastqsanger.gz
	SRR8832556.fastq.gz	Fastqsanger.gz
	SRR8832557.fastq.gz	Fastqsanger.gz
	SRR8832558.fastq.gz	Fastqsanger.gz

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QuantSeq analysis in the hippocampus of WT and PHF2 t/g mice

Project description:Long-term memory formation is attributed to experience-dependent gene expression. Dynamic changes in histone methylation status are essential for epigenetic regulation of memory consolidation-related genes. Here, we demonstrated that plant homeodomain finger protein 2 (PHF2) histone demethylase is upregulated in the mouse hippocampus during experience and plays an essential role in memory formation. QuantSeq analysis was performed to examine differential gene expression in the hippocampus of WT and PHF2 t/g mice. Transgenic mice were created by injecting the CMV-Flag-PHF2 vector into fertilized eggs from C57BL6 mice. Transgenic lines were established from 9 founders that were identified via PCR-based genotyping. Among the transgenic lines, mice with high PHF2 expressed brains were singled out for breeding. First, selected heterozygote males were bred with heterozygote females which produced homozygote, heterozygote and wild littermates. Since it is difficult to differentiate between hetero and homo mice with genotyping, we separated homo mice from hetero mice by breeding each of hetero and homo mice with wild type mice and confirming the genotypes of their offspring. In other words, hetero mice bred with wild type mice would have both wild type and hetero genotype of offspring, while homo mice bred with wild type mice would only have hetero genotype of offspring. Through this process, we particularly selected the homo mice and this transgenic line was used and maintained for this experiment.

2019-07-27 | GSE129148 | GEO

Quantseq 3'mRNA-seq in LESCs from WT and TXNIP-/- mice

Project description:Quantseq 3'mRNA-seq in LESCs from WT and TXNIP-/- mice

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Hi-C in neural stem cells before and after Phf2 KO

Project description:To model and characterize the chromatin regulatory landscape in Neural stem cell before and after Phf2 knockout, we performed HiC to map large-scale 3D architectural rewiring in WT and Phf2-KO NSC.

2024-05-10 | GSE243810 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of hippocampus transcriptomes from WT and miR-301a-/- mice

Project description:Purpose: we used next generation sequencing to analyze gene expression profiles of hippocampus from WT and miR-301a-/- mice. The goals of this study are to compare the different gene expression profiles of hippocampus between WT and miR-301a-/- mice.

2022-01-28 | GSE194389 | GEO

Expression data from liver samples overxpressing either the GFP or Phf2

Project description:The GFP or Phf2 were overexpressed in the liver of C57Bl6/J mice through adenoviral gene delivery. Mice were studied in the fed state 3 weeks later. We used microarray analysis to detail the global programme of gene expression underlying Phf2 overexpression and identified distinct classes of up and down regulated genes.

2015-10-01 | GSE61575 | GEO

Transcriptome analysis in PHf2 KO C2C12 cells

Project description:To evaluate the role of Phf2 in C2C12 myotube, we generated Phf2 KO C2C12 cells and analyzed the transcriptome by RNA-sequencing.

2024-02-29 | GSE226618 | GEO

Hippocampus CA1 pyramidal cells Transcriptomic profile in WT and Fmr1 KO mice, using Wfs1-CreERT2:RiboTag:Frm1 knockout and wildtype mice

Project description:Comparing WT mice to a mouse model of mental retardation, this work identifies genes which display differences in ribosome-bound mRNAs, in hippocampus CA1 pyramidal cells. These genes products are potent functional components of neuronal plasticity and hippocampus-dependent memory.

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Single-cell RNA sequencing reveals a role of Phf2 in promoting the exit of postnatal neural stem cell from shallow quiescence.

Project description:Dentate gyrus single cell mRNA profiles of 30-day-old wild-type (WT) and Phf2 conditional knockout (Phf2−/−) mice were generated by single cell sequencing. We performed data filtering: i) for the genes expressed in at least 30 cells and cells with detected expression of at least 200 genes and no more than 8000 genes; ii) cells with the percentage of expressed mitochondrial genes no more than 10%. Potential cell doublets were filtered out using scrublet (https://pypi.org/project/scrublet/). Single cell clustering was done using scanpy package (https://scanpy.readthedocs.io/en/stable/).

2024-07-23 | GSE173293 | GEO

PAS-seq from layer of hippocampus (ENCSR147WNH)

Project description:Mouse hippocampus QuantSeq 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

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ChIP-seq experiment of PHF2 and H3K9me2 in NSCs

Project description:Histone H3 lysine 9 methylation (H3K9me) is essential for cellular homeostasis; however, its contribution to development is not well established. Here, we demonstrate that the H3K9me2 demethylase PHF2 is essential for neural progenitor proliferation in vitro and for early neurogenesis in the chicken spinal cord. Using genome-wide analyses and biochemical assays we show that PHF2 controls the expression of critical cell cycle progression genes, particularly those related to DNA replication, by keeping low levels of H3K9me3 at promoters. Accordingly, PHF2 depletion induces R-loop accumulation that leads to extensive DNA damage and cell cycle arrest. These data reveal a role of PHF2 as a guarantor of genome stability that allows proper expansion of neural progenitors during development.

2019-09-10 | GSE122263 | GEO

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