Long read single cell RNA-Seq
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB37531 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4921180_1.fastq.gz | Fastqsanger.gz | |||
| ERR4921180_2.fastq.gz | Fastqsanger.gz | |||
| ERR4921190_1.fastq.gz | Fastqsanger.gz | |||
| ERR4921190_2.fastq.gz | Fastqsanger.gz | |||
| ERR4922130.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 60 |
Similar Datasets
Project description:This study benchmarks bulk and single-cell long-read RNA sequencing technologies in a human neuronal model of Fragile X syndrome. NGN2-induced neurons were generated from patient-derived iPSCs carrying a silenced FMR1 gene (FXS line E3) and an isogenic CRISPR-corrected rescue line (IsoB11) in which FMR1 expression is restored. These conditions provide a defined system to evaluate transcript detection and quantification across sequencing platforms. Bulk and single-cell RNA-seq datasets were generated using Illumina short-read sequencing and long-read sequencing from Pacific Biosciences (PB) and Oxford Nanopore Technologies (ONT). Single-cell libraries were prepared using the 10x Genomics Chromium platform. ERCC and SIRV spike-in controls were added to bulk samples to enable benchmarking of transcript quantification accuracy. Three biological replicates were sequenced for each condition. The dataset enables cross-platform comparisons of transcript detection, quantification methods, transcript length biases, and sequencing depth requirements for long-read transcriptomic analyses.
2025-03-30 | E-MTAB-16805 | biostudies-arrayexpress
Project description:Single cell RNA-profiling in tandem with short-read sequencing (SR-scRNA-seq) has revolutionized the field of transcriptomics, permitting a highly granular view on cellular blood and tissue composition and the construction of human cell atlases. However, discrimination between various transcript isoforms remains challenging. Here we developed single cell long-read isoform sequencing (scLIS-seq), a scRNA-seq workflow based on Smart-seq3xpress (SS3X) cDNA generation and Oxford Nanopore Technologies PromethION sequencing. Using scLIS-seq, we profiled the long-read transcriptomes of Jurkat and HEK293T cells and compared its performance to SS3X starting from the identical cDNA. This dataset refers to the raw and processed data of the Smart-seq3xpress and scLIS-seq experiments of the Jurkat and HEK293T cells.
2025-12-31 | E-MTAB-15047 | biostudies-arrayexpress
Project description:LocusMasterTE: long-read assisted short-read RNA-seq TE quantification [long]
| PRJNA935368 | ENA
Project description:LocusMasterTE: long-read assisted short-read TE quantification [short]
| PRJNA935371 | ENA
Project description:Background: Single-cell CRISPR screens have transformed functional genomics by enabling scalable, systematic investigation of gene function. Despite this, transcriptional complexity has largely been overlooked, with studies focusing on gene-level effects rather than isoforms. Methods capable of capturing splicing and isoform usage have emerged, including long-read sequencing and alternative library preparation strategies, but their suitability for large-scale perturbation screens remains unevaluated. Results: We compare two single-cell library preparation methods (5' 10x Genomics and Parse Biosciences Evercode) across Illumina short-read, Oxford Nanopore Technologies, and PacBio long-read sequencing, applying CRISPRi to silence three genes with distinct regulatory roles (DDX6, GEMIN5 and GFI1B) in K562 cells. While short-read methods can detect some alternative splicing events, only long-read sequencing consistently captures isoform-level changes. Although Parse Evercode provided even coverage across transcripts, we observed strong enrichment of intronic reads, limiting its utility for splicing analysis. The primary constraint of long-read approaches was depth: approximately 21 million reads are required for 80% saturation of splicing events in a single perturbation, underscoring the need for higher-throughput methods. Despite these limitations, we show that GEMIN5 perturbation produced modest differential expression but the most extensive splicing changes, an effect invisible to gene-level analysis, highlighting the importance of extending CRISPR screens to isoform-level readouts. Conclusions: We provide a practical framework for isoform-level analysis in single-cell CRISPR screens, identifying both the capabilities and current limitations of available approaches. As perturbation studies scale, long-read sequencing will be essential for comprehensive functional interpretation, capturing biology missed by gene-level analysis.
2026-05-19 | GSE330222 | GEO
Project description:Alternative splicing significantly contributes to transcriptome complexity and has critical implications for cellular functions. Recent advancements in single-cell isolation and capture techniques have enabled high-throughput quantification of gene expression at single-cell resolution. Long-read sequencing technologies can further be combined with single-cell technologies and enable an unambiguous identification of complete exon structures. Several computational methods have been developed to specifically address bioinformatics challenges associated with the processing of long read scRNA-seq data. Evaluating and comparing these computational methods becomes crucial. The goal of this study was to benchmark state-of-the-art computational tools for single-cell and spatial long-read transcriptomics. The scRNA-seq data were generated from two tumors developed by a mouse model, and designated as MPNST1 and MPNST2. Data were obtained by using the 10X Genomics technology, then generating sequencing libraries using either Illumina, Oxford Nanopore Technology (ONT) or scNaUmi-Seq protocols. Raw data were obtained after sequencing the libraries on Illumina, MinION or PromethION sequencing platforms. The two Illumina data were uploaded as part of the related submission E-MTAB-14222, with sample MPNST1 corresponding to 2020_23 and MPNST2 to 2022_26. This current submission contains the four long-read raw data et the data processed using the wf-single-cell pipeline. For the additional processed data, please refer to https://github.com/GenomiqueENS/scKenver.
2025-08-26 | E-MTAB-15190 | biostudies-arrayexpress
Project description:This study benchmarks bulk and single-cell long-read RNA sequencing technologies in a human neuronal model of Fragile X syndrome. NGN2-induced neurons were generated from patient-derived iPSCs carrying a silenced FMR1 gene (FXS line E3) and an isogenic CRISPR-corrected rescue line (IsoB11) in which FMR1 expression is restored. These conditions provide a defined system to evaluate transcript detection and quantification across sequencing platforms. Bulk and single-cell RNA-seq datasets were generated using Illumina short-read sequencing and long-read sequencing from Pacific Biosciences (PB) and Oxford Nanopore Technologies (ONT). Single-cell libraries were prepared using the 10x Genomics Chromium platform. ERCC and SIRV spike-in controls were added to bulk samples to enable benchmarking of transcript quantification accuracy. Three biological replicates were sequenced for each condition. The dataset enables cross-platform comparisons of transcript detection, quantification methods, transcript length biases, and sequencing depth requirements for long-read transcriptomic analyses.
2026-03-25 | E-MTAB-16791 | biostudies-arrayexpress
Project description:Single-cell RNA sequencing analysis has recently provided snapshots of gene expression of specific cell types and enabled cell types classification within an heterogenous population. As well as transcriptional changes, alternative splicing events and modifications of components of splicing machinery actively contributes in shaping cellular phenotype as well as ageing process and diseases occurence. Current high-throughput single-cell RNA sequencing methods may lack information on cell-specific isoform expression, missing key aspects of cell biology. In the present work we introduce a novel approach using the 10X Genomics Chromium to generate short-read (Illumina) and long-read (Pacific Biosciences Sequel II) RNA-sequencing libraries from the same single cells. This approach produced single cell parallel transcriptional and splicing profiling that demonstrates for the first time cell-type specific isoform expression and alterations at transcriptional levels associated with ageing in haematopoietic stem and progenitor cells
2022-12-31 | GSE166709 | GEO
Project description:DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts.
2024-08-19 | GSE246836 | GEO
Project description:Short-read and long-read single-cell sequencing capture distinct perturbation effects in CRISPR screens
| PRJNA1463191 | ENA