Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single molecule and long-read RNA-seq

ABSTRACT: A single molecule and long-read view of the diverse human transcriptome

PROVIDER: PRJEB3969 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR279822_1.fastq.gz	Fastqsanger.gz
	ERR279823_subreads.fastq.gz	Fastqsanger.gz
	ERR279824_1.fastq.gz	Fastqsanger.gz
	ERR279825_1.fastq.gz	Fastqsanger.gz
	ERR279826_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 55

Similar Datasets

Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm

Project description:Sperm contributes diverse RNAs to the zygote. While sperm small RNAs have been shown to impact offspring phenotypes, our knowledge of the sperm transcriptome, especially the composition of long RNAs has been limited by the lack of sensitive, high-throughput experimental techniques that can distinguish intact RNAs from fragmented RNAs, known to abound in sperm. Here, we integrate single-molecule long-read sequencing with short-read sequencing to detect sperm intact RNAs (spiRNAs). We identify 3,440 spiRNA species in mice and 4,100 in humans. The spiRNA profile consists of both mRNAs and long non-coding RNAs, is evolutionarily conserved between mice and humans, and displays an enrichment in mRNAs encoding for ribosome. In sum, we characterize the landscape of intact long RNAs in sperm, paving the way for future studies on their biogenesis and functions. Our experimental and bioinformatics approaches can be applied to other tissues and organisms to detect intact transcripts.

2021-01-11 | GSE137490 | GEO

Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm

Project description:Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm

| PRJNA565724 | ENA

Long-range single-molecule mapping of chromatin accessibility in eukaryotes

Project description:Active regulatory elements in eukaryotes are typically characterized by an open, nucleosome-depleted chromatin structure; mapping areas of open chromatin has accordingly emerged as a widely used tool in the arsenal of modern functional genomics. However, existing approaches for profiling chromatin accessibility are limited by their reliance on DNA fragmentation and short read sequencing, which leaves them unable to provide information about the state of chromatin on larger scales or reveal coordination between the chromatin state of individual distal regulatory elements. To address these limitations, we have developed a method for profiling accessibility of individual chromatin fibers at multi-kilobase length scale (SMAC-seq, or Single-Molecule long-read Acessible Chromatin mapping sequencing assay), enabling the simultaneous, high-resolution, single-molecule assessment of the chromatin state of distal genomic elements. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases (CpG and GpC 5-methylcytosine (5mC) and N6-methyladenosine (m6A) enzymes) and the ability of long-read single-molecule nanopore sequencing to directly read out the methylation state of individual DNA bases. Applying SMAC-seq to the budding yeast Saccharomyces cerevisiae, we demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule protection footprints of nucleosomes and transcription factors, and quantify the correlation between the chromatin states of distal genomic elements

2019-12-01 | GSE128290 | GEO

Detecting PKD1 variants in Polycystic Kidney Disease patients by single-molecule long-read sequencing

Project description:A genetic diagnosis of autosomal dominant polycystic kidney disease (ADPKD) is challenging. However, long-read single-molecule sequencing has been shown to be a reliable alternative strategy that could overcome PKD1 complexities. Using long-read sequencing to characterize a cohort of 19 patients with ADPKD, we developed an approach that provided high sensitivity in identifying PKD1 pathogenic variants, with a diagnostic yield of 94.7%. Reliable screening of ADPKD patients in a single test without interference of PKD1 homologous sequences is now possible.

| EGAS00001002106 | EGA

Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Project description:We produced an extensive transcript catalog for LCLs of 5 primate species by leveraging isoform sequencing and short-read RNA-seq. The curated transcriptomes were used to assist mass spectrometry protein identifications.

2022-05-31 | PXD031213 | Pride

Long read single cell RNA-Seq

Project description:Integrated long- and short-read single-cell RNA-sequencing

| PRJEB37531 | ENA

Third-generation long-read whole-genome sequencing of Dux knockout mouse

Project description:We applied Single Molecule Real-Time long-read whole-genome sequencing in Dux knockout mouse and confirmed the success of our Dux knockout mouse model.

2019-07-31 | GSE134830 | GEO

Single-molecule sequencing of maize and sorghum developmental tissues

Project description:In this study, we compared the transcriptome map of maize and sorghum using PacBio single-molecule long-read sequencing from multiple matched tissues in each species. Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared the transcriptional profiles of both protein-coding and non-coding transcripts in matched tissues using large-scale single-molecule sequencing from 130 RSII cells and 5 Sequel cells, as well as deep short-read RNA sequencing. The use of multiple size-fractionated libraries (<1 kb, 12 kb, 23 kb, 35 kb, and >5 kb) enhanced our capture of non-redundant transcripts in these tissues.

2018-04-05 | E-MTAB-5957 | biostudies-arrayexpress

High-resolution transcriptome analysis with long-read RNA sequencing

Project description:Ongoing improvements to next generation sequencing technologies are leading to longer sequencing read lengths, but a thorough understanding of the impact of longer reads on RNA sequencing analyses is lacking. To address this issue, we generated and compared two RNA sequencing datasets of differing read lengths -- 2x75 bp (L75) and 2x262 bp (L262) -- and investigated the impact of read length on various aspects of analysis, including the performance of currently available read-mapping tools, gene and transcript quantification, and detection of allele-specific expression patterns. Our results indicate that, while the scalability of read-mapping tools and the cost-effectiveness of long read protocol is an issue that requires further attention, longer reads enable more accurate quantification of diverse aspects of gene expression, including individual-specific patterns of allele-specific expression and alternative splicing. Two RNA-Seq datasets of differing read lengths (2x262 bp and 2x75 bp)

2014-09-25 | E-GEOD-57862 | biostudies-arrayexpress

LocusMasterTE: long-read assisted short-read RNA-seq TE quantification [long]

Project description:LocusMasterTE: long-read assisted short-read RNA-seq TE quantification [long]

| PRJNA935368 | ENA