Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets [sc_spleen]

ABSTRACT: The goal of this study was to optimize single-cell long-read RNA sequencing in pancreatic islets to enable accurate isoform-level gene expression analysis. We aimed to overcome key technical limitations—including insufficient read lengths, high error rates, and transcript abundance bias—that have hindered long-read sequencing in single cells. Specifically, we compared 5’ and 3’ library preparation strategies and evaluated transcript depletion methods to improve detection of low-abundance isoforms. Our objective was to establish a robust protocol that enhances isoform identification and reveals differential transcript usage across pancreatic islet cell types.

ORGANISM(S): Mus musculus

PROVIDER: GSE295352 | GEO | 2026/01/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets [sc_islet]

Project description:The goal of this study was to optimize single-cell long-read RNA sequencing in pancreatic islets to enable accurate isoform-level gene expression analysis. We aimed to overcome key technical limitations—including insufficient read lengths, high error rates, and transcript abundance bias—that have hindered long-read sequencing in single cells. Specifically, we compared 5’ and 3’ library preparation strategies and evaluated transcript depletion methods to improve detection of low-abundance isoforms. Our objective was to establish a robust protocol that enhances isoform identification and reveals differential transcript usage across pancreatic islet cell types.

2026-01-26 | GSE295353 | GEO

Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets [bulk_islet]

2026-01-26 | GSE295351 | GEO

Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets [bulk_islet]

Project description:Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets [bulk_islet]

| PRJNA1254252 | ENA

Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets [sc_spleen]

Project description:Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets [sc_spleen]

| PRJNA1254258 | ENA

Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets [sc_islet]

Project description:Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets [sc_islet]

| PRJNA1254251 | ENA

Accurate isoform quantification by joint short- and long-read RNA-sequencing [short reads]

Project description:Accurate quantification of transcript isoforms is crucial for understanding gene regulation, functional diversity, and cellular behavior. Existing methods using either short-read (SR) or long-read (LR) RNA sequencing have significant limitations: SR sequencing provides high depth but struggles with isoform deconvolution, while LR sequencing offers isoform resolution at the cost of lower depth, higher noise, and technical biases. Addressing this gap, we introduce Multi-Platform Aggregation and Quantification of Transcripts (MPAQT), a generative model that combines the complementary strengths of different sequencing platforms to achieve state-of-the-art isoform-resolved transcript quantification, as demonstrated by extensive simulations and experimental benchmarks. Applying MPAQT to an in vitro model of human embryonic stem cell differentiation into cortical neurons, followed by machine learning-based modeling of mRNA abundance determinants, reveals the role of untranslated regions (UTRs) in isoform regulation through isoform-specific interactions with RNA-binding proteins that modulate mRNA stability. These findings highlight MPAQT's potential to enhance our understanding of transcriptomic complexity and underline the role of splicing-independent post-transcriptional mechanisms in shaping the isoform and exon usage landscape of the cell.

2024-07-10 | GSE271528 | GEO

Accurate isoform quantification by joint short- and long-read RNA-sequencing [long reads]

2024-07-10 | GSE271527 | GEO

Long-read isoform sequencing reveals Aroclor1260-induced isoform expression in mouse liver

Project description:Long-term exposure to polychlorinated biphenyls (PCBs) including the mixture of PCBs in Aroclor1260 (Ar1260) results in metabolic dysfunction-associated steatotic liver disease (MASLD) in mice and humans. Previously, we reported that chronic (34 wks.) exposure of normal low fat diet (LFD)-fed male mice to Ar1260 resulted in twelve hepatic RNA modifications. We confirmed the downregulation NRF2 (Nfe2l2) network pathway associated with human liver diseases. Proteomic analysis of these same liver samples identified Ar1260 exposure-associated changes in protein abundance including altered selenoproteins: GPX4 and SELENBP2 were increased and SELENOS and SELENOF were reduced. Alternative splicing (AS) has been implicated in MASLD. Here we used long-read isoform sequencing (IsoSeq) to and differential transcript usage (DTU) to specific DTU gene differences depending on the severity of liver injury with Ar1260.

2026-03-03 | GSE308889 | GEO

Hypatia: a statistical framework for single-cell RNA isoform data analysis

Project description:Cells express distinct splicing isoforms in normal physiology and disease. Long-read single-cell RNA-sequencing (LR-scRNAseq) enables isoform quantification at single-cell resolution. However, methods to assess isoform complexity between cell populations are lacking. To address this, we present Hypatia, a toolkit for analyzing isoform usage shifts, diversity, and expression. Using simulated data, we establish a framework for comparative analysis. Using three LR-scRNAseq data sets, we identify widespread transcript-level heterogeneities across cells.

2026-03-05 | GSE310974 | GEO

Long-read isoform sequencing reveals Aroclor1260-induced isoform expression in mouse liver

Project description:Long-read isoform sequencing reveals Aroclor1260-induced isoform expression in mouse liver

| PRJNA1333336 | ENA