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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kansl1-/- MEFs Transcriptomes

ABSTRACT: We report the application of RNA-sequence in WT and Kansl1-deleted MEF cells with 3 biological replicates. We mapped over 42 million sequence reads per sample to the mouse genome (build mm10).

ORGANISM(S): Mus musculus

PROVIDER: GSE176424 | GEO | 2021/06/10

REPOSITORIES: GEO

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kansl1-/- MEFs Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kansl1-/- MEFs Transcriptomes

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KANSL1 CHIP-sequence analysis in HeLa cells

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Mouse models of 17q21.31 microdeletion and microduplication syndromes highlight the importance of Kansl1 for cognition.

Project description:Koolen-de Vries syndrome (KdVS) is a multi-system disorder characterized by intellectual disability, friendly behavior, and congenital malformations. The syndrome is caused either by microdeletions in the 17q21.31 chromosomal region or by variants in the KANSL1 gene. The reciprocal 17q21.31 microduplication syndrome is associated with psychomotor delay, and reduced social interaction. To investigate the pathophysiology of 17q21.31 microdeletion and microduplication syndromes, we generated three mouse models: 1) the deletion (Del/+); or 2) the reciprocal duplication (Dup/+) of the 17q21.31 syntenic region; and 3) a heterozygous Kansl1 (Kans1+/-) model. We found altered weight, general activity, social behaviors, object recognition, and fear conditioning memory associated with craniofacial and brain structural changes observed in both Del/+ and Dup/+ animals. By investigating hippocampus function, we showed synaptic transmission defects in Del/+ and Dup/+ mice. Mutant mice with a heterozygous loss-of-function mutation in Kansl1 displayed similar behavioral and anatomical phenotypes compared to Del/+ mice with the exception of sociability phenotypes. Genes controlling chromatin organization, synaptic transmission and neurogenesis were upregulated in the hippocampus of Del/+ and Kansl1+/- animals. Our results demonstrate the implication of KANSL1 in the manifestation of KdVS phenotypes and extend substantially our knowledge about biological processes affected by these mutations. Clear differences in social behavior and gene expression profiles between Del/+ and Kansl1+/- mice suggested potential roles of other genes affected by the 17q21.31 deletion. Together, these novel mouse models provide new genetic tools valuable for the development of therapeutic approaches.

2017-04-14 | GSE80311 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Control and FoxM1-knockdown C2C12 Transcriptomes

Project description:Purpose:To identify FoxM1-dependent genes and the molecular pathways involved in the regulation of muscle stem cells function, we performed RNA-Sequence of C2C12 from shControl and shFoxM1 cells. Methods: C2C12 mRNA and lncRNA profiles of shControl and shFoxM1 cells (quiescent or activated states) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. Results:Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample to the mouse genome (build mm10) and identified 49,586 transcripts in the control C2C12 and FoxM1-knockdown C2C12 with BWA workflow. Conclusions: Our results represents the first detailed analysis of C2C12 transcriptomes and found that knockdown of FoxM1 perturbed multiple mRNA pathways, as well as for novel lncRNA pathways.

2017-09-01 | GSE102685 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type Young and Old muscle Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare Young and Old muscles transcriptome profiling (RNA-seq) to optimal high-throughput data analysis Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10) and identified 24799 genes. Among them, 95.7% of the genes displayed the similar expression level in both young and old muscles.2% of genes (501) were significantly up-regulated and 2.3% of genes (584) were significantly down-regulated. p value <0.05.

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Next Generation Sequencing Facilitates Quantitative Analysis of interferon stimulated MEFs Transcriptomes [RNA-Seq]

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived interferon-stimulated MEF cells transcriptome profiling (RNA-seq).

2018-08-28 | GSE89349 | GEO

Next-Generation Sequencing Facilitates Quantitative Analysis of Interferon-Stimulated MEFs Transcriptomes [RNA-Seq]

2023-01-01 | GSE174476 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of the Role of nuclear protein DEK in hematopoietic stem cells [RNA-seq]

Project description:Purpose:To identify genes and the molecular pathways involved in the DEK regulating hematopoietic stem cells (HSC) in mice, we performed RNA-Sequence of HSC freshly sorted from mice. Methods: mRNA profiles of HSC in Dekfl/fl (floxp) and Dekfl/fl,Tie2-Cre (cKO) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. Results:Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (build mm10) and identified 33299 transcripts in HSC (the floxp and cKO group) with BWA workflow. Conclusions: Our results represent the first detailed analysis of HSC transcriptomes in Dek-knockout mice and found that DEK regulated multiple mRNA pathways in HSC.

2021-02-22 | GSE166431 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of SCs in mice exposure to exercise

Project description:Purpose:To identify genes and the molecular pathways involved in the regulation of muscle satellite cells (SCs) in mice exposure to running exercise, we performed RNA-Sequence of SCs in untrained (Con) and trained mice (Exe). Methods: mRNA profiles of SCs in untrained (Con) and trained mice (Exe) (running exercise, 4 days/week, 30 min/day at 12 m/min) were generated by deep sequencing, in quadruplicate, using Illumina HiSeq 2000. Results:Using an optimized data analysis workflow, we mapped about 9 million sequence reads per sample to the mouse genome (build mm10) and identified 9031 transcripts in SCs (the control and exercise group) with BWA workflow. Conclusions: Our results represent the first detailed analysis of SCs transcriptomes in mice exposure to running exercise and found that exercise regulated multiple mRNA pathways in SCs.

2020-06-08 | GSE128651 | GEO

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