Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome and epigenome dynamic of the clonal heterogeneity of human induced pluripotent stem cells for cardiac differentiation [ATAC-Seq]

ABSTRACT: Transcriptome and epigenome dynamic of the clonal heterogeneity of human induced pluripotent stem cells for cardiac differentiation [ATAC-Seq]

PROVIDER: PRJNA1083905 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28227808_1.fastq.gz	Fastqsanger.gz
	SRR28227808_2.fastq.gz	Fastqsanger.gz
	SRR28227809_1.fastq.gz	Fastqsanger.gz
	SRR28227809_2.fastq.gz	Fastqsanger.gz
	SRR28227810_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Transcriptome and epigenome dynamic of the clonal heterogeneity of human induced pluripotent stem cells for cardiac differentiation [RNA-seq]

Project description:Transcriptome and epigenome dynamic of the clonal heterogeneity of human induced pluripotent stem cells for cardiac differentiation [RNA-seq]

| PRJNA1083443 | ENA

Transcriptome and epigenome dynamic of the clonal heterogeneity of human induced pluripotent stem cells for cardiac differentiation [ATAC-Seq]

Project description:Human induced pluripotent stem cells (hiPSCs) generate multiple clones with inherent heterogeneity, leading to variations in their differentiation capacity. Previous studies have primarily addressed line-to-line variations in differentiation capacity, leaving a gap in the comprehensive understanding of clonal heterogeneity. Here, we aimed to identify predictive biomarkers for cardiomyocyte differentiation capacity by integrating transcriptomic, epigenomic, endogenous retroelement, and protein kinase phosphorylation profiles. We generated multiple clones from a single donor and validated that these clones exhibited comparable levels of pluripotent markers. These clones were then classified into two groups based on their differentiation capacity: productive clone (PC) and non-productive clone (NPC). We performed RNA sequencing and assay for transposase-accessible chromatin with sequencing (ATAC-seq). NPC was enriched in vasculogenesis and cell adhesion, accompanied by elevated ERK1/2 signaling pathway phosphorylation. Conversely, PC exhibited enrichment in embryonic organ development and transcription factor activation, accompanied by increased chromatin accessibility. Integrative analysis of RNA sequencing and ATAC-seq revealed 14 candidate genes correlated with cardiac differentiation propensity. Notably, TEK and SDR42E1 were upregulated in NPC. Our integrative profiles enhance the understanding of clonal heterogeneity and highlight two novel biomarkers associated with cardiomyocytes differentiation. This insight may facilitate the identification of suboptimal hiPSC clones, thereby mitigating adverse outcomes in clinical applications.

2024-12-16 | GSE260883 | GEO

Transcriptome and epigenome dynamic of the clonal heterogeneity of human induced pluripotent stem cells for cardiac differentiation [RNA-seq]

2024-12-16 | GSE260767 | GEO

Transcriptome and epigenome dynamics of the clonal heterogeneity of human induced pluripotent stem cells for cardiac differentiation.

Project description: Not available

| S-EPMC11635083 | biostudies-literature

Clonal heterogeneity in melanoma

Project description:Genetic heterogeneity is an important feature of solid tumors, however it is often assumed that most cancer cell lines are genetically homogeneous. A disparity in genetic complexity between cell lines and the disease they model could result in problems such as in vitro preclinical experiments overstating the effectiveness of putative therapeutics. We therefore derived clonal sublines by single cell cloning of in house derived early passage melanoma cell lines (LM-MEL-series), and compared their genomes to each other and the parental cell line using Illumina 610-Quad SNP arrays.

2013-09-08 | E-MTAB-1753 | biostudies-arrayexpress

Clonal heterogeneity of mantle cell lymphoma revealed by array comparative genomic hybridization

Project description:The existence of clonal heterogeneity of mantle cell lymphoma based on genomic aberration evaluated by log2 ratio(clinical samples)

2012-07-30 | E-MTAB-1076 | biostudies-arrayexpress

Cerebral organoids display dynamic clonal growth with lineage replenishment

Project description:Cerebral organoids display dynamic clonal growth with lineage replenishment

| PRJNA883958 | ENA

Intratumoral heterogeneity and clonal evolution induced by HPV integration

Project description:Intratumoral heterogeneity and clonal evolution induced by HPV integration

| PRJNA1006805 | ENA

Intratumoral heterogeneity and clonal evolution induced by HPV integration

Project description:Intratumoral heterogeneity and clonal evolution induced by HPV integration

| PRJNA1273205 | ENA

Co-mapping Clonal and Transcriptional Heterogeneity in Somatic Evolution via GoT-Multi.

Project description:Somatic evolution leads to clonal heterogeneity, which fuels cancer progression and therapy resistance. To decipher the consequences of clonal heterogeneity, we require a method that deconvolutes complex clonal architectures and their downstream transcriptional states. We developed Genotyping of Transcriptomes for multiple targets and sample types (GoT-Multi), a high-throughput, formalin-fixed paraffin-embedded (FFPE) tissue-compatible single-cell multi-omics for co-detection of multiple somatic genotypes and whole transcriptomes. We developed an ensemble-based machine learning pipeline to optimize genotyping. We applied GoT-Multi to frozen or FFPE samples of Richter transformation, a progression of chronic lymphocytic leukemia to therapy-resistant large B cell lymphoma. GoT-Multi detected heterogeneous cancer cell states with genotypic data of 27 mutations, enabling clonal architecture reconstruction linked with their transcriptional programs. Distinct subclonal genotypes, including therapy-resistant mutations, converged on an inflammatory state. Other subclones displayed enhanced proliferation and/or MYC program. Thus, GoT-Multi revealed that distinct genotypic identities may converge on similar transcriptional states to mediate therapy resistance.

2025-09-03 | GSE294045 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data