Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GEO accession GSE275610 is currently private and is scheduled to be released on Jun 05, 2029.

ABSTRACT: GEO accession GSE275610 is currently private and is scheduled to be released on Jun 05, 2029.

PROVIDER: PRJNA1152220 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR33859900.fastq.gz	Fastqsanger.gz
	SRR33860000.fastq.gz	Fastqsanger.gz
	SRR33860100.fastq.gz	Fastqsanger.gz
	SRR33860200.fastq.gz	Fastqsanger.gz
	SRR33860300.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6991

Similar Datasets

scRNA-seq and snATAC-seq reveal differentiation trajectories of several pancreatic islet induction protocols

Project description:With the help of scRNA-seq and snATAC-seq, we unraveled the differentiation trajectories and gene co-expression networks of current islet induction protocols. Inspired by our understanding to in vivo pancreatogenesis, we improved the current protocol by inducing human anterior lip endoderm at stage 2 and promoting ventral pancreas fate. This refined differentiation protocol simplifies the existing multistage processes and generates higher-quality sc-islets with larger beta cell proportion and enhanced function of glucose regulation, which are validated by scRNA-seq and snATAC-seq.

2025-10-20 | GSE275610 | GEO

Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk [snATAC-seq]

Project description:Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type–specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell–derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics.

2021-01-14 | GSE160472 | GEO

snATAC-seq data from single cell multiomics (paired snRNA-seq+snATAC-seq) of human colorectal cancer liver metastatic samples

Project description:These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Tumour microenvironment cell types and cancer cell states were identified using 10x Genomics Multiome (paired snRNA-seq + snATAC-seq). snATAC-seq data is uploaded here.

2025-04-22 | E-MTAB-13652 | biostudies-arrayexpress

Trajectories of microbiome derived bile acids in early life insights into the progression to islet autoimmunity

Project description:Here, we analyzed early life MCBA patterns and their link to islet autoimmunity. We quantified 110 MCBAs in 303 stool samples collected longitudinally (3 to36 months) from children who developed one or more islet autoantibodies and controls who remained autoantibody negative.

2025-08-05 | MSV000098739 | MassIVE

Functional gene regulatory networks and broad applications of the human expandable pancreatic progenitor-islet system [snATAC-seq]

Project description:Functional gene regulatory networks and broad applications of the human expandable pancreatic progenitor-islet system [snATAC-seq]

| PRJNA1197359 | ENA

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols

Project description:We sequenced mRNA according to several library prep protocols with known mixtures of two species of Drosophila in order to establish linear response in each protocol.

2015-01-07 | GSE64673 | GEO

Functional gene regulatory networks and broad applications of the human expandable pancreatic progenitor-islet system [snATAC-seq]

Project description:Investigating the precise gene regulatory programs directing pancreatic differentiation provides insights into the mechanisms of pancreatic development and diabetes progression. Here, we performed integrated single-cell multi-omic analyses of the expandable pancreatic progenitor (ePP)-islet system. We defined the dynamic transcriptomic and chromatin landscapes of pancreatic differentiation, inferred the sophisticated gene regulatory networks (GRNs) that govern ePP self-renewal, endocrine specification and islet function, and identified the essential roles and interesting mechanisms of the NKX2.2-CLEC16A/endosomal pathway axis during cell-fate transitions. We have obtained interesting observations that are human specific not observed in mouse models (e.g., CLEC16A-related diabetes mechanisms), and further took advantage of the ePP-islet system to identify pharmacological rescuers. Notably, this study highlights the ePP-islet system as a very powerful platform for uncovering the molecular mechanisms of cell fate decision and rich information for further optimizing the differentiation process. With further optimization and better understanding, the ePP-islet system will undoubtedly have very broad applications, including disease modeling, drug discovery, and regenerative medicine.

2026-01-12 | GSE284103 | GEO

Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk

Project description:Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type-specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell-derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics.

2021-01-14 | GSE160474 | GEO

Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk [RNA-seq]

2021-01-14 | GSE160473 | GEO