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

ABSTRACT: 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

ORGANISM(S): Mus musculus

PROVIDER: GSE96645 | GEO | 2018/09/12

REPOSITORIES: GEO

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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

Next Generation Sequencing Analysis of gene expression profile in Dgcr8 conditional KO embryonic hearts

Project description:Purpose: To compare the transcriptome of wild type and Mesp1Cre+/Dgcr8-/- embryonic heart at embryonic stage E8.5 and E9.5 Methods: For mRNA analysis of embryonic heart during development, total RNA of E8.5 and E9.5 heart were extracted with TRIZOL, and 100ng total RNA was reverse transcribed and amplified by Smart-seq 2 protocol as described (Picelli et al., 2014). Duplicated biological samples were analyzed using Illumina HiSeq2500, Clean reads were mapped to mouse genome (mm9) using BWA software. Results: Genes significantly differentially expressed in the CKO cardiac tube at E9.5 compared with wild type were identified. Conclusions: Dgcr8 CKO caused important gene expression changes in E9.5 embryonic heart tube

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Cardiac Sex Differences in the Transcriptome of C57 Male and Female E9.5 Hearts

Project description:Purpose: The goals of this study are to compare E9.5 male and female C57 mouse embryonic hearts transcriptome profiling (RNA-seq) to conclude cardiac sex differences at the mRNA level. Methods: mRNA profiles of E9.5 male and female C57 mouse embryonic hearts were generated by deep sequencing, n=4 for each sex, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10) and identified 16,460 transcripts in the mouse 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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RNAseq analysis on e9.5 mutant mouse hearts

Project description:We report RNAseq analysis on RNA from e9.5 hearts of Asb2 mutant and Asb2.Flna double mutants with controls. The goal of this study is to identify Asb2 downstream targets in the heart as well as targets that are corrected in the Asb2.Flna double mutant vs the Asb2 singe mutants.

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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

Single cell RNA Sequencing Analysis of Gene Expression Profile in Dgcr8 Conditional KO Embryonic Hearts

Project description:Purpose: To compare the single cell transcriptome of wild type and Mesp1Cre+/Dgcr8-/- embryonic heart at embryonic stage E9.5 Methods: For single cell sample preparation, Ventricular part of E9.5 heart tubes were dissected and digested into single cells by 0.04% Trypsin combined with 0.05% Collagenase IV, and then transferred into DMEM containing 10% fetal bovine serum for termination. After washed in PBS without Ca2+, the single cells were manually transferred into cell lysis buffer with a mouth pipette. Total RNA was reverse transcribed and amplified using Smart-seq2 protocol (Picelli et al., 2014), followed by Tn5 tagmentation and PCR enrichment to generate libraries using TruePrep DNA Library Prep Kit V2 for illumina (Vazyme, TD501-503) according to the manufacturer’s suggested protocol. Clean reads were mapped to mouse genome (mm10) using Salmon. Results: Genes significantly differentially expressed in the E9.5 Dgcr8 cKO single cardiomyocyte compared with wild type group were identified. Conclusions: Dgcr8 cKO caused important gene expression changes in E9.5 cardiomyocytes at single cell level

2018-09-12 | GSE110265 | GEO

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

Quantitative Proteomic Profiling of Murine Embryonic Heart Development Reveals a Role for the Mevalonate Pathway in Cardiomyocyte Proliferation [Heart_RNAseq]

Project description:Purpose: The goals of this study are to characterize and analyze the emrbyonic heart transcriptome profiling (RNA-seq) at E9.5, E10.5, E12.5, E14.5 and E16.5. Methods: mRNA profiles of E9.5, E10.5, E12.5, E14.5 and E16.5 C57/Bl6 mouse embryonic hearts were generated by deep sequencing, n=3 or 4 for each age, using Illumina HiSeq2500. Results: Using an optimized data analysis workflow, we mapped at least 36 million sequence reads per sample to the mouse genome (build mm10) and identified 17,537 transcripts in the mouse hearts.

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Expression data from outflow region at E9.5

Project description:A high concentration of maternal retinoic acid (RA), the active derivative of vitamin A, is well known as a teratogenic agent which can cause developmental defects. Our previous studies have shown that the maternal administration of RA to mice within a narrow developmental window induces outflow tract (OFT) septum defects, which closely resembles human transposition of the great arteries (TGA), although the responsible factors and pathogenic mechanisms of the TGA induced by RA still remain unknown. To identify the candidate genes involved in the altered development of the OFT in RA-induce TGA model, we isolated the RNA from E9.5 control and RA-treated OFT regions, and performed a microarray analysis. Approximately 200 outflow tract region were isolated from control and RA-treated embryos (embryonic day 9.5). We sought to obtain the candidate genes involved in the altered development of the OFT in RA-induce heart defects.

2011-11-08 | E-GEOD-33472 | biostudies-arrayexpress

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