Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1127255 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29543170_1.fastq.gz | Fastqsanger.gz | |||
| SRR29543171_1.fastq.gz | Fastqsanger.gz | |||
| SRR29543172_1.fastq.gz | Fastqsanger.gz | |||
| SRR29543173_1.fastq.gz | Fastqsanger.gz | |||
| SRR29543174_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Preparation of libraries for circular RNA sequencing with Oxford Nanopore long-read sequencing
2022-08-09 | GSE197872 | GEO
Project description:a chromosome-level nuclear genome and organelle genomes of the alpine snow alga Chloromonas typhlos were sequenced and assembled by integrating short- and long-read sequencing and proteogenomic strategy
| PXD056928 |
Project description:Objectives: To perform long-read transcriptome and proteome profiling of pathogen-stimulated peripheral blood mononuclear cells (PBMCs) from healthy donors. We aim to discover new transcripts and protein isoforms expressed during immune responses to diverse pathogens. Methods: PBMCs were exposed to four microbial stimuli for 24 hours: the TLR4 ligand lipopolysaccharide (LPS), the TLR3 ligand Poly(I:C), heat-inactivated Staphylococcus aureus, Candida albicans, and RPMI medium as negative controls. Long-read sequencing (PacBio) of one donor and secretome proteomics and short-read sequencing of five donors were performed. IsoQuant was used for transcriptome construction, Metamorpheus/FlashLFQ for proteome analysis, and Illumina short-read 3’-end mRNA sequencing for transcript quantification. Results: Long-read transcriptome profiling reveals the expression of novel sequences and isoform switching induced upon pathogen stimulation, including transcripts that are difficult to detect using traditional short-read sequencing. We observe widespread loss of intron retention as a common result of all pathogen stimulations. We highlight novel transcripts of NFKB1 and CASP1 that may indicate novel immunological mechanisms. In general, RNA expression differences did not result in differences in the amounts of secreted proteins. Interindividual differences in the proteome were larger than the differences between stimulated and unstimulated PBMCs. Clustering analysis of secreted proteins revealed a correlation between chemokine (receptor) expression on the RNA and protein levels in C. albicans- and Poly(I:C)-stimulated PBMCs. Conclusion: Isoform aware long-read sequencing of pathogen-stimulated immune cells highlights the potential of these methods to identify novel transcripts, revealing a more complex transcriptome landscape than previously appreciated.
2023-09-16 | PXD045237 | Pride
Project description:To identify aberrant splicing isoforms and potential neoantigens, we performed full-length cDNA sequencing of lung adenocarcinoma cell lines using a long-read sequencer MinION. We constructed a comprehensive catalog of aberrant splicing isoforms and detected isoform-specific peptides using proteome analysis.
2020-12-09 | PXD019915 | JPOST Repository
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: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: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:We sequenced DNA from a bulk of Col x Ler F2 hybrid plants (WT and recq4) using Nanopore long-read sequencing and identified crossover sites with COmapper. For nanopore sequencing of gDNA from 1,000 pooled seedlings, 10-day-old seedlings were ground in liquid nitrogen using a mortar and pestle. The ground tissue was resuspended in four volumes of CTAB buffer (1% [w/v] CTAB, 50 mM Tris-HCl pH 8.0, 0.7 M NaCl, 10 mM EDTA) and incubated at 65°C for 30 min. Following chloroform extraction, isopropanol precipitation and removal of RNAs as above, the gDNA pellet was resuspended in 150 μl TE (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA) buffer and gDNA was quantified using a Qubit dsDNA Broad Range assay kit (Thermo Fisher, Q32853). Nine micrograms of gDNA from pollen or seedlings was used to construct a nanopore long-read sequencing library using a Ligation Sequencing Kit V14 (Nanopore, SQK-LSK114). The libraries were sequenced using a PromethION platform (BGI, Hong Kong).
2024-08-19 | E-MTAB-14368 | biostudies-arrayexpress
Project description:Long read SMRT cDNA sequencing of nascent RNA from exponentially growing S. cerevisiae and S. pombe cells was employed to obtain transcription elongation and splicing information from single transcripts. Nascent RNA was prepared from the yeast chromatin fraction (Carrillo Oesterreich, Preibisch, Neugebauer, Mol Cell 2010). The nascent 3â?? end was labeled with a 3â?? DNA adaptor through ligation. The adaptor sequence served as template for full-length reverse transcription and double-stranded cDNA was obtained in a PCR (gene-specific or transcriptome-wide). SMRT DNA sequencing libraries were prepared subsequently. Nascent RNA profiles for mainly intron-containing genes were generated with long-read SMRT cDNA sequencing.
2016-03-24 | E-GEOD-70906 | biostudies-arrayexpress
Project description:We sequenced DNA from the leaves of ten Col x Ler F1 hybrid plants (WT and recq4) using Nanopore long-read sequencing and identified crossover sites with COmapper. These data were used as a negative control for COmapper, as no crossover sites were expected to be detected. For nanopore sequencing of gDNA from leaves, leaves from 10 5-week-old plants were ground in liquid nitrogen using a mortar and pestle. The ground tissue was resuspended in four volumes of CTAB buffer (1% [w/v] CTAB, 50 mM Tris-HCl pH 8.0, 0.7 M NaCl, 10 mM EDTA) and incubated at 65°C for 30 min. Following chloroform extraction, isopropanol precipitation and removal of RNAs as above, the gDNA pellet was resuspended in 150 μl TE (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA) buffer and gDNA was quantified using a Qubit dsDNA Broad Range assay kit (Thermo Fisher, Q32853). Nine micrograms of gDNA from pollen or seedlings was used to construct a nanopore long-read sequencing library using a Ligation Sequencing Kit V14 (Nanopore, SQK-LSK114). The libraries were sequenced using a PromethION platform (BGI, Hong Kong).
2024-08-19 | E-MTAB-14381 | biostudies-arrayexpress