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Single-nuclear multiome (RNA & ATAC) profiling of Pax3-Cre lineage traced endothelium from E9.5 mouse embryos and bulk ATAC-seq from E13.5 mouse embryos

ABSTRACT: Single-nuclear multiome (RNA & ATAC) profiling of Pax3-Cre lineage traced endothelium from E9.5 mouse embryos and bulk ATAC-seq from E13.5 mouse embryos

PROVIDER: PRJNA1156231 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30535417_1.fastq.gz	Fastqsanger.gz
	SRR30535417_2.fastq.gz	Fastqsanger.gz
	SRR30535418_1.fastq.gz	Fastqsanger.gz
	SRR30535418_2.fastq.gz	Fastqsanger.gz
	SRR30535419_1.fastq.gz	Fastqsanger.gz

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Single-nuclear multiome (RNA & ATAC) profiling of Pax3-Cre lineage traced endothelium from E9.5 mouse embryos and bulk ATAC-seq from E13.5 mouse embryos

Project description:Background: The formation of the lymphatic system has been a subject of controversy for over a century. Although the accepted view is that lymphatic endothelial cells originate exclusively from veins, there have been reports of non-venous derived lymphatics in multiple tissues. Methods: We performed single-nuclear multiome sequencing analyses on 3,801 individual nuclei isolated from Pax3Cre/+;Rosa26tdTomato mouse embryos at E9.5, the temporal window in which lymphatic endothelium initially emerges. Additionally, we performed bulk ATAC-seq analyses following the OmniATAC protocol on FACS-sorted ECs from Pax3Cre/+;Rosa26tdTomato embryos at E13.5. Results: These analyses revealed the existence of angioblasts which arise from paraxial mesoderm and directly differentiate into lymphatic endothelium. Our findings support the notion that lymphatic endothelial cells also have non-venous origins and explain the discrepancies between previous studies.

2024-10-19 | GSE276282 | GEO

Transcriptomic analysis of E9.5 mouse embryos

Project description:Transcriptomic analysis of E9.5 mouse embryos

| PRJNA727827 | ENA

Gene expression in E9.5 trunks comparing wt with Arid3b-null embryos

2014-10-07 | GSE62071 | GEO

Gene expression in E9.5 heads comparing wt with Arid3b-null embryos

2014-10-07 | GSE62070 | GEO

Gene expression in E9.5 hearts comparing wt with Arid3b-null embryos

2014-10-07 | GSE62069 | GEO

Gene expression in E9.5 heads comparing wt with Arid3b-null embryos

Project description:We have analysed and compared mRNA expression between wt embryos and embryos deficient for Arid3b in E9.5 heads, with the aim of identifying differentially expressed genes that could give us a clue to the functions of Arid3b during development. Heads were dissected from E9.5 embryos (including head and first branchial arch). Four wild-type and four mutant embryos were collected and pooled for each of the microarray triplicates.

2014-10-07 | E-GEOD-62070 | biostudies-arrayexpress

Gene expression in E9.5 hearts comparing wt with Arid3b-null embryos

Project description:We have analysed and compared mRNA expression between wt embryos and embryos deficient for Arid3b in E9.5 hearts, with the aim of identifying differentially expressed genes that could give us a clue to the functions of Arid3b during development. Hearts were dissected from E9.5 embryos (including the heart tube and the pharyngeal mesoderm and endoderm located beneath). Four wild-type and four mutant embryos were collected and pooled for each of the microarray triplicates.

2014-10-07 | E-GEOD-62069 | biostudies-arrayexpress

Gene expression in E9.5 trunks comparing wt with Arid3b-null embryos

Project description:We have analysed and compared mRNA expression between wt embryos and embryos deficient for Arid3b in E9.5 trunks, with the aim of identifying differentially expressed genes that could give us a clue to the functions of Arid3b during development. Trunks were dissected from E9.5 embryos (including the body from the otic vesicle to somite 15 and forelimbs). Four wild-type and four mutant embryos were collected and pooled for each of the microarray triplicates.

2014-10-07 | E-GEOD-62071 | biostudies-arrayexpress

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.

2024-04-18 | GSE260690 | GEO

Genome wide RNA-seq analysis of E9.5 Smchd1 wild type and mutant embryos

Project description:We report the deregulation of expression in E9.5 male mouse embryos are that homozygous for a mutant allele of the Smchd1 gene (ie Smchd1MommeD1/MommeD1).

2013-07-03 | GSE44665 | GEO

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