Next-generation sequencing Facilitates Quantitative Analysis of Wild Type and Arid1a haploinsufficiency mice excitatory neuron Transcriptomes and Genome-wide maps of chromatin state in Wild Type and Ar id1a Haploinsufficiency mice in excitatory neuron

ABSTRACT: Purpose: The goals of this study are to compare WT and Arid1a in excitatory neuron transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) differentially expressed genes and find target genes. We performed chromatin-immunoprecipitation coupled to sequencing (ChIP-seq) to dissect the relationship between the differentially expressed genes and the occupancy of H3K27ac and Arid1a. Methods: Excitatory neurons mRNA profiles of adult wild-type (WT) and Arid1a Het mice were generated by deep sequencing, in duplicate,using Illumina HiSeq 2500 system.All RNA-Seq data were aligned to mouse genome version mm10 using Salmon (v.1.1.0) .We use cluster software and Euclidean distance matrix for the hierarchical clustering analysis of the expressed gene and sample program at the same time, the clustering results can be viewed with javaTreeview. qRT–PCR validation was performed using SYBR Green assays. we performed ChIP-seq using freshly isolated P14 from Wild Type and EED-/- cerebellar tissues . DNA libraries generated from ChIP-DNA and input-DNA were deep-sequenced using HiSeq single-end 50bp. Results:Only transcripts that showed more than 1.5-fold differential expression compared to control were subjected to relevance network analysis. 3815 candidate genes that were differentially expressed with biological functional groups as compared between WT and Arid1a Het mice .We found that the enrichment of H3K27acwas decreased in Arid1a Het mice. Conclusions: Our study represents the first detailed analysis of Wild Type and Arid1a haploinsufficiency mice excitatory neuron transcriptomes, with two biologic replicates, generated by RNA-seq technology. We report the application of ChIP-sequencing technology for high-throughput profiling of histone modifications in excitatory neurons.

ORGANISM(S): Mus musculus

PROVIDER: GSE198916 | GEO | 2022/03/21

REPOSITORIES: GEO