biostudies-arrayexpressElisa BalmasHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15710This dataset was generated to investigate the role of two DNA-binding factors, CTCF and GATA4, in early cardiac specification. Three WTC11-derived hiPSC lines were employed, each carrying a stably integrated shRNA construct. Two of the constructs specifically target CTCF and GATA4, while the third expresses a scrambled, non-targeting shRNA that serves as a control. All shRNA systems are driven by a tetracycline-inducible promoter, enabling conditional knockdown. Each of the three cell lines was differentiated into 3D cardiac organoids patterned toward right ventricle and atrium fates. Differentiations were carried out for 7.5 days, both in the presence and absence of tetracycline, thereby providing an isogenic control for each knockdown condition. For every condition, two independent differentiations were performed, ensuring biological replication.biostudies-arrayexpressNucleic Acid Extraction - RNA was extracted with the ZymoResearch kit and converted to cDNA. For each sample, 400 ng of total RNA was used as input.Sample Collection - cardiac organoids (Atria or Right ventricle) were collected at day 7.5 in biological duplicate.Sample Treatment - half of the samples (indicated with TET) were treated with tetracycline 1 ug/ml since the split of hiPSCs immediately before differentiationLibrary Construction - TruSeq® Stranded mRNA Library Prep (20020594) and IDT for Illumina – TruSeq RNA UD Indexes (20020591) Illumina® Stranded mRNA Prep, Ligation (20040534)Sequencing - MGI T7 flow cell PE100 V3, performing 100 bp paired-end cycling.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Reads were trimmed to remove the adapter CTGTCTCTTATACACATCT and an extra trimming of 1 bp at 3' and 5 at 5' was perfomed to remove artifacts of the library. Trimmed reads were aligned over an indexed reference genome built on the ENSEMBL GRCh38.111 using STAR 2.7.11b in GeneCounts modeData Transformation - filtering for reads with at least 3 counts in a minimum of 2 samples, and filtering for protein coding genes using DeSEQ2. Reads were then normalised in TPM usin the ADImpute R package, and the read length file obtained with gtftools (-l function)MetabolomicsUnknownTranscriptomicsGenomicsProteomicsDNBSEQ-T7nullHomo sapiensSara BianchiElisa BalmasfalseBulk RNA sequencing of cardiac organoids differentiated from hiPSC-derived cell lines with knockdown of factors involved in early cardiac specificationThis dataset was generated to investigate the role of two DNA-binding factors, CTCF and GATA4, in early cardiac specification. Three WTC11-derived hiPSC lines were employed, each carrying a stably integrated shRNA construct. Two of the constructs specifically target CTCF and GATA4, while the third expresses a scrambled, non-targeting shRNA that serves as a control. All shRNA systems are driven by a tetracycline-inducible promoter, enabling conditional knockdown. Each of the three cell lines was differentiated into 3D cardiac organoids patterned toward right ventricle and atrium fates. Differentiations were carried out for 7.5 days, both in the presence and absence of tetracycline, thereby providing an isogenic control for each knockdown condition. For every condition, two independent differentiations were performed, ensuring biological replication.2025-10-14T00:00:00Z2026-05-28T10:05:21.176Z2025-10-14T08:57:55.98ZE-MTAB-15710ERP182073EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969