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ATAC-seq of E9.5 WT and Smyd1-KO mouse hearts

ABSTRACT: ATAC-seq of E9.5 WT and Smyd1-KO mouse hearts

PROVIDER: PRJNA1082682 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28197390_1.fastq.gz	Fastqsanger.gz
	SRR28197390_2.fastq.gz	Fastqsanger.gz
	SRR28197391_1.fastq.gz	Fastqsanger.gz
	SRR28197391_2.fastq.gz	Fastqsanger.gz
	SRR28197392_1.fastq.gz	Fastqsanger.gz

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ATAC-seq of E9.5 WT and Smyd1-KO mouse hearts

Project description:Purpose: The goal of this study is to identify the differential cardiac chromatin accessibility between WT and Smyd1 null (Smyd1-KO) hearts at E9.5 using ATAC-seq. Methods: Four hearts at E9.5 were pooled per genotype per replicate, and were then dissociated into single cells. 40,000 viable cells were taken for were lysed to isolate nuclei, which were treated with Tn5 transposase (Nextera DNA Sample Prep Kit, Illumina) to isolate DNA. Fragmented DNA was then amplified using bar-coded PCR primers and libraries were seuqenced. Results: 25851 differential peaks (2-fold change) were identified between E9.5 WT and Smyd1-KO hearts.

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Project description:Purpose: The goal of this study is to identify the differential cardiac transcriptome profiling between WT and Smyd1 null (Smyd1-KO) hearts at E9.5 using RNA-seq. Methods: mRNA profiles of E9.5 WT and Smyd1-KO mouse hearts were generated by deep sequencing, n=3 for each genotype, using Illumina HiSeq2500. The sequence reads were aligned to the mm10 reference genome using STAR via the bcbio-nextgen RNA-sequencing pipeline. Differential gene expression was determined by DEseq2. Results: 1756 genes were differentially expressed between WT and Smyd1-KO hearts [adjusted P value <0.05, |log2(Fold Change)| > 0.5], with 1130 upregulated and 626 downregulated in E9.5 Smyd1-KO hearts.

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