{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Tobias Bønnelykke"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16670"],"description":["Ventricular septal defects are among the most common forms of congenital heart defects. The aim of this project is to compare the transcriptome of cells in the interventricular region of the mouse heart at embryonic day 13.5 in control and mutant embryos carrying a conditional dominant negative retinoic acid receptor (R26-RARa403) with a defect in interventricular septal morphogenesis. The driver of the conditional expression is the anterior second heart field cre line: Mef2c-AHF-Cre."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - The interventricular septum of control (Rosa26-RARα403/+) and mutant (Mef2c-AHF-CreTg+; Rosa26-RARα403/+) E13.5 mouse hearts were microdissected in 1x RNase/DNase free PBS (Gibco, 14190-169) and flash frozen in liquid nitrogen. Samples were genotyped by PCR of the tails.","Library Construction - RNA quantity and -quality were measured using Agilent RNA 6000 Nano chips on a BioAnalyzer (Agilent). All RINs were ≥ 9.40. 250ng of RNA per sample was used for preparing mRNA libraries with the Kapa mRNA HyperPrep (Roche, #KR1352-v5.17) kit according to manufacturer's instructions.","Sequencing - Paired-end sequencing of 75 base pair reads was performed on an Illumina NextSeq 500 platform using equimolar amounts of libraries per sample. The mean sequencing depth per sample was 57.5 million reads.","Nucleic Acid Extraction - To isolate RNA, TRIzol-chloroform extraction (Invitrogen, 15596026) was performed followed by purification using the RNeasy Micro kit (QIAGEN, 74004). A piston was used to initially lyse the tissue. Extracted RNA was stored at -70oC."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - After mapping, the number of reads per feature was determined using Stringtie v1.3.1c (PMID: 25690850). Normalization and differentially expressed genes were calculated using DESeq2 (PMID: 25516281) and p values were adjusted for multiple testing using the Benjamini-Hochberg procedure.","Sequence Alignment - FASTQ files were mapped to the mouse reference genome GRCm38/mm10 with the addition of sequences for Cre (NC_005856.1), R26RARα403 (Nucleotide 1 to 1739 of NM_001024809.4) and Sv40-polyA (PMID: 1644817) using STAR v2.7.2b (PMID: 26334920), and bam files were indexed using Sambamba v0.6.6 (PMID: 25697820)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Robert Kelly","Tobias Bønnelykke"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of the interventricular septum in mouse heart at embryonic day 13.5 in control and mutant embryos carrying a conditional dominant negative retinoic acid receptor (R26-RARa403) with a defect in interventricular septal morphogenesis","description":"Ventricular septal defects are among the most common forms of congenital heart defects. The aim of this project is to compare the transcriptome of cells in the interventricular region of the mouse heart at embryonic day 13.5 in control and mutant embryos carrying a conditional dominant negative retinoic acid receptor (R26-RARa403) with a defect in interventricular septal morphogenesis. The driver of the conditional expression is the anterior second heart field cre line: Mef2c-AHF-Cre.","dates":{"release":"2026-09-14T00:00:00Z","modification":"2026-09-14T14:32:29.379Z","creation":"2026-02-24T20:51:10.307Z"},"accession":"E-MTAB-16670","cross_references":{"ENA":["ERP189509"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}