biostudies-arrayexpressJunqing ZhangMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16538This study aims to investigate the regulatory role of N-acetylneuraminate lyase (Npl) during the stepwise differentiation of embryonic stem cells (ESCs) into functional cardiomyocytes (CMs). We performed a high-throughput transcriptomic analysis comparing wild-type (WT) and Npl knockout (KO) cell lines at four critical developmental stages: undifferentiated embryonic stem cells (D0), embryoid bodies (D2), mesoderm progenitors (D4), and mature cardiomyocytes (D14). By examining the gene expression profiles across these time points, we seek to identify the molecular mechanisms and downstream signaling pathways through which Npl modulates mesoderm specification and cardiac lineage commitment. Our findings provide insights into the transcriptional landscape of early cardiac development and the potential involvement of Npl in congenital heart defects.biostudies-arrayexpressSample Collection - ells were harvested at designated time points (D0, D2, D4, and D14). The culture medium was aspirated and discarded. Cell layers were gently washed once with ice-cold DPBS to remove residual serum and media components. Cells were then collected by mechanical scraping using a cell scraper in the presence of DPBS or lysis buffer.Library Construction - RNA samples were sent to Novogene (UK) for library construction, quality control and sequencing.Nucleic Acid Extraction - Total RNA was extracted from cells using QIAzol Lysis Reagent (Qiagen) followed by purification with the Reasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration and purity were assessed using a Nanodrop 2000 spectrophotometer (Thermo Scientific), with samples exhibiting A260/A280 ratios between 1.8 and 2.1 and A260/A230 ratios > 2.0 considered suitable for downstream analysis. RNA integrity was further verified using an Agilent 5400 Fragment Analyzer, with RNA integrity numbers (RIN) > 8.0 required for library preparation.Sequencing - RNA samples were sent to Novogene (UK) for library construction, quality control and sequencing.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw data (raw reads) in fastq format was processed to remove reads containing adapter, reads containing ploy-N and low-quality reads from raw data. All the downstream analyses were based on the clean data with high quality. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome (mm39) using Hisat2. The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNAMus musculusJunqing ZhangPilar Ruiz-LozanofalseTime-course analysis of gene expression during mouse embryonic stem cell differentiation into cardiomyocytes: impact of Npl deficiency.This study aims to investigate the regulatory role of N-acetylneuraminate lyase (Npl) during the stepwise differentiation of embryonic stem cells (ESCs) into functional cardiomyocytes (CMs). We performed a high-throughput transcriptomic analysis comparing wild-type (WT) and Npl knockout (KO) cell lines at four critical developmental stages: undifferentiated embryonic stem cells (D0), embryoid bodies (D2), mesoderm progenitors (D4), and mature cardiomyocytes (D14). By examining the gene expression profiles across these time points, we seek to identify the molecular mechanisms and downstream signaling pathways through which Npl modulates mesoderm specification and cardiac lineage commitment. Our findings provide insights into the transcriptional landscape of early cardiac development and the potential involvement of Npl in congenital heart defects.2026-06-01T00:00:00Z2026-06-01T01:03:00.908Z2026-01-16T19:11:20.576ZE-MTAB-16538ERP187670EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184