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Transcriptomic analysis in E9.5 heart tubes identify genes dysregulated in Sox7-null heart tubes

ABSTRACT: Transcriptomic analysis in E9.5 heart tubes identify genes dysregulated in Sox7-null heart tubes

PROVIDER: PRJNA708272 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13913405_1.fastq.gz	Fastqsanger.gz
	SRR13913405_2.fastq.gz	Fastqsanger.gz
	SRR13913406_1.fastq.gz	Fastqsanger.gz
	SRR13913406_2.fastq.gz	Fastqsanger.gz
	SRR13913407_1.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis in E9.5 heart tubes identify genes dysregulated in Sox7-null heart tubes

Project description:RNA-seq differential gene expression analysis was accomplished in E9.5 pooled(n = approximately 30) microdissected heart tubes from Sox7-null embryos and a wild-type littermates.

2022-03-01 | GSE168543 | GEO

ChIP-Seq on SOX7-V5 tagged mouse embryos at E9.5 and E10.5

Project description:We intended to identify the potential binding targets of SOX7 in mouse during development (E9.5-E10.5)

2022-12-30 | E-MTAB-12320 | biostudies-arrayexpress

Next Generation Sequencing Analysis of miRNA expression profile in E9.5 mouse embryonic heart

Project description:Purpose: To identify miRNA expresssion profiles in E9.5 mouse embryonic heart Methods: Total RNA of E9.5 heart were extracted with TRIZOL, miRNA deep sequencing were performed in using Illumina Hiseq 2500, SE50 (RIBOBIO, http://www.ribobio.com/), producing over 10 million reads from each sample. Clean reads were mapped to mouse genome (mm9), using miRDeep2 Results: MiRNAs that were highly expressed in E9.5 embryonic heart were identified Conclusions: Results provide insight into the role of miRNAs function in E9.5 embryonic heart development

2018-09-12 | GSE96645 | GEO

Transcriptome analysis identifies genes dysregulated in Sox7-null embryos at E8.5

Project description:To identify genes that are differentially expressed in the developing mouse embryo as a result of SOX7 deficiency, we performed bulk RNA-seq on Sox7-null and wild-type embryos harvested at E8.5.

2023-07-24 | GSE236846 | GEO

Next Generation Sequencing Analysis of gene expression profile in E9.5 Mesp1Cre/+/Dgcr8-/- embryonic heart cells transfected with NC miRNA and miR-541 mimics

Project description:Purpose: To compare the E9.5 Dgcr8 conditional knockout embryonic heart cells transfected with NC miRNA and miR-541 mimics Methods: In vitro cultured E9.5 Dgcr8 conditional KO heart cells transfected with miR-541-5p and NC miRNA were extracted with TRIZOL 48hrs after transfection, and 10ng total RNA was reverse transcribed and amplified by Smart-seq2 protocol as described (Picelli et al., 2014). Duplicated biological samples were analyzed using Illumina HiSeqX10, Clean reads were mapped to mouse genome (mm9) using BWA software. Results: Genes differentially expressed in E9.5 Dgcr8 cKO embryonic heart cells transfected with NC miRNA and miR-541 were identified. Conclusions: miRNA-541 significantly changes the gene expression profiles of E9.5 Dgcr8 cKO embryonic heart cells and promote the cardiac function

2018-09-12 | GSE96647 | GEO

Sox7 regulates lineage decisions in cardiovascular progenitor cells

Project description:Specification of the mesodermal lineages requires a complex set of morphogenetic events orchestrated by interconnected signaling pathways and gene regulatory networks. The transcription factor Sox7 has critical functions in differentiation of multiple mesodermal lineages, including cardiac, endothelial, and hematopoietic. Using a doxycycline-inducible mouse embryonic stem cell (mESC) line, we have previously shown that expression of Sox7 in cardiovascular progenitor cells promotes expansion of endothelial progenitor cells. Here, we show that the ability of Sox7 to promote endothelial cell fate occurs at the expense of the cardiac lineage. Using ChIP-Seq coupled with ATAC-Seq we identify downstream target genes of Sox7 in cardiovascular progenitor cells and, by integrating these data with transcriptomic analyses, we define Sox7-dependent gene programs specific to cardiac and endothelial progenitor cells. Further, we demonstrate a protein-protein interaction between SOX7 and GATA4 and provide evidence that Sox7 interferes with the transcriptional activity of Gata4 on cardiac genes. In addition, we show Sox7 modulates WNT and BMP signaling during cardiovascular differentiation. Our data represent the first genome-wide analysis of Sox7 function and reveal a critical role for Sox7 in regulating signaling pathways that affect cardiovascular progenitor cell differentiation.

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SOX7 ChIP-seq in HUVECs

Project description:We investigated SOX7 binding events on the chromatin under basal conditions in human umbilical vein endothelial cells, upon overexpression of human SOX7-mCherry and immunoprecipitating mCherry. Cells overexpressing only the mCherry tag were used as negative control condition, and peaks called here were substracted from the SOX7-mCherry peaks.

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Gata6 induced XEN-like cells w/o Sox7

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Project description:As a transcription factor, SOX7 suppresses cancer development. However, only a few genes were demonstrated as SOX7-activated targets in cancer-irrelevant contexts. We used microarray chips to determine SOX7 target genes in breast cancer cells and discovered multiple signaling pathways altered by ectopic SOX7. We also investigated several genes for their roles in SOX7-mediated tumor suppression. Our study innovatively revealed SOX7 target gene profile in a cancer-relevant context and identified several SOX7-repressed target genes.

2018-02-26 | GSE111122 | GEO

Gata6 induced XEN-like cells w/o Sox7

Project description:To understand the role of Sox7 in primitive endoderm differentiation, we compare the gene expression pattern of Sox7 (+/-) and Sox7 (-/-) ES cells with or without dexamethasome (Dex) treatment. Because these ES cells harbour Gata6-GR transgene, Dex treatment forces ES cells differentate into XEN-like cells. As Sox7 (-/-) ES cells can differentiate into XEN-like cell by morphology, we assessed genome wide gene expression pattern. Sox7 (+/-) ES cells and Sox7 (-/-) ES cells are forced to differentiate into XEN-like cells by Gata6-GR transgene. To compare the gene expression, we collected RNA samples at day4 with or without dexamethasone treatment from each genotype.

2015-09-14 | E-GEOD-66971 | biostudies-arrayexpress

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