Project description:The mammalian heart is divided into four chambers by septa that arose during vertebrate evolution to isolate the systemic and pulmonary circulation. Septation defects are the most common cause of congenital heart defects, however, it is not fully understood how they are formed during cardiogenesis. Expression of a conditional dominant negative retinoic acid receptor in a subset of the heart using a Mef2c-AHF-Cre line leads to failure of muscular interventricular septum (IVS) morphogenesis resulting in a deep interventricular cleft and a bifid ventricular phenotype that emerges by E12.5. To understand the genetic changes that drive this morphogenesic defect, we have performed single cell RNA sequencing in control and mutant hearts at E11.5, one day prior to the phenotypic onset. 10 controls IVS and 8 mutant IVS were pooled separately prior to dissociation.

2026-09-14 | E-MTAB-17365 | biostudies-arrayexpress

Single-cell RNA-seq data of cardiac cells derived from a human induced pluripotent stem cell control line

Project description:Characterization of cell-type diversity obtained after cardiac differentiation of hiPSC using single-cell RNA-Seq.

2022-12-05 | E-MTAB-11817 | biostudies-arrayexpress

Mouse, pig, and human atherosclerotic lesions have common and distinct mesenchymal cell populations

Project description:The single-cell RNA-seq experiment aims to explore the cell-type composition of right coronary artery plaques to provide an overview of human-like atherosclerosis. The PCSK9 transgenic minipigs were subjected to 15 months of HFHC diet (HFHC group f, n=4; m, n=1). At the time of euthanasia, plaque parts without media were quickly processed and analyzed by scRNA-sequencing.

2025-08-30 | E-MTAB-15464 | biostudies-arrayexpress

Systematic Single-Cell Dissection of Cell Cycle and TGFβ-Induced State Transitions Underlying Gemcitabine Resistance in 3D Pancreatic Tumor Tissue

Project description:Study Description for ArrayExpress Submission: This study investigates cellular heterogeneity and mechanisms of gemcitabine resistance in pancreatic cancer using single-cell RNA sequencing of PANC-1 cells cultured in a 3D environment (and 2D control). Cells were seeded onto a decellularized porcine intestinal matrix to mimic the tumor microenvironment. The experiment analyzed transcriptional profiles before gemcitabine treatment, with particular attention to invasion and resistance states induced by TGFβ. Single-cell RNA-seq was used to map the transcriptional landscape of 3D pancreatic tumor tissues, capturing cell state transitions, differentiation trajectories, and resistance-associated profiles. The analysis identified cell cycle–dependent resistance signatures (late S to G2(/M) phase), tissue differentiation-associated states, and TGFβ-induced epithelial-to-mesenchymal transition (EMT) pathways contributing to chemoresistance. The dataset includes untreated samples with and without TGFβ stimulation, enabling identification of attractor states and transitional paths leading to gemcitabine resistance. This study provides insight into tumor cell plasticity and dedifferentiation in a 3D matrix environment, supporting early diagnostic and therapeutic research in pancreatic cancer.

2026-07-10 | E-MTAB-17360 | biostudies-arrayexpress

Single-cell RNA sequencing data of human dorsal forebrain organoids derived from three iPSC lines

Project description:This dataset contains single-cell RNA sequencing data generated from nine dorsal forebrain organoids collected at day 90 of differentiation. The organoids were derived from three human induced pluripotent stem cell lines: KOLF2.1J, BIONi010-C, and HMGU1. The primary objective of the study was to explore potential neurodevelopmental and differentiation-related differences among these lines, with a specific focus on the KOLF2.1J line, in which previously undetected structural variants were identified through optical genome mapping and long-read sequencing.

2026-08-03 | E-MTAB-17432 | biostudies-arrayexpress

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