Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Transcriptome sequencing of Pachyrhizus erosus across different tissues using both short-read and full-length sequencing approaches to identify the genes involved in rotenone biosynthesis

PROVIDER: PRJNA1193469 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR31583477_1.fastq.gz	Fastqsanger.gz
	SRR31583477_2.fastq.gz	Fastqsanger.gz
	SRR31583478_1.fastq.gz	Fastqsanger.gz
	SRR31583478_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 21

Similar Datasets

Pachyrhizus erosus

Project description:Pachyrhizus erosus overview

| PRJNA906218 | ENA

Project description:Pachyrhizus erosus/tuberosus sequencing

| PRJNA713851 | ENA

Pachyrhizus erosus cultivar:PI 574551 01 SD

Project description:Pachyrhizus erosus, de novo genome assembly

| PRJNA817234 | ENA

Project description:A chromosome-level genome for Pachyrhizus erosus

| PRJNA1002465 | ENA

Tachypleus tridentatus

Project description:Full-length and short read transcriptome data of Tachypleus tridentatus

| PRJNA577185 | ENA

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

Project description:Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computational methods. Long-read sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) bypass the transcript reconstruction challenges of short-reads. Here we describe TALON, the ENCODE4 pipeline for analyzing PacBio cDNA and ONT direct-RNA transcriptomes. We apply TALON to three human ENCODE Tier 1 cell lines and show that while both technologies perform well at full-transcript discovery and quantification, each one displayed distinct artifacts. We further apply TALON to mouse cortical and hippocampal transcriptomes and find that a substantial proportion of neuronal genes have more reads associated with novel isoforms than with annotated ones. These data show that TALON is a technology-agnostic long-read transcriptome discovery and quantification pipeline capable of tracking both known and novel transcript models, as well as their expression levels, across datasets for both simple studies and in larger projects. These properties will enable TALON users to move beyond the limitations of short-read data to perform isoform discovery and quantification in a uniform manner on existing and future long-read platforms.

2020-03-18 | GSE147118 | GEO

Direct long-read RNA sequencing of Raji cells

Project description:To identify full-length cap-to-poly(A) mRNA isoforms of CD20 and rule out reverse transcription artifacts which are common in cDNA-seq approaches, long-read Oxford Nanopore direct RNA sequencing was performed on the Raji cell line.

2023-12-08 | GSE243920 | GEO

Proteogenomic and expression profiling of virulent and attenuated Gallid alphaherpesvirus 1

Project description:Virulent (1874C5) and attenuated (vaccine strain LaryngoVac) strains of infectious laryngotracheitis virus (ILTV) were characterized in vivo for transcript expression via short-read mRNA-Seq and in vitro for transcript and protein expression using full-length cDNA sequencing and high-resolution LC-MS/MS.

2025-02-08 | MSV000097080 | MassIVE

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

Project description:Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computational methods. Long-read sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) bypass the transcript reconstruction challenges of short-reads. Here we describe TALON, the ENCODE4 pipeline for analyzing PacBio cDNA and ONT direct-RNA transcriptomes. We apply TALON to three human ENCODE Tier 1 cell lines and show that while both technologies perform well at full-transcript discovery and quantification, each technology has its distinct artifacts. We further apply TALON to mouse cortical and hippocampal transcriptomes and find that a substantial proportion of neuronal genes have more reads associated with novel isoforms than annotated ones. The TALON pipeline for technology-agnostic, long-read transcriptome discovery and quantification tracks both known and novel transcript models as well as expression levels across datasets for both simple studies and larger projects such as ENCODE that seek to decode transcriptional regulation in the human and mouse genomes to predict more accurate expression levels of genes and transcripts than possible with short-reads alone.

2019-06-15 | GSE132766 | GEO

PacBio long-read RNA-sequencing to identify differentially expressed genes and repetitive elements between Wild Type RBM4 KO HAP1 cell line samples

Project description:Since short reads from Illumina RNA-seq data are challenging to map to repetitive elements , we wanted to confirm the bulk RNA-seq findings using an orthogonal method, namely, using the long read technology of Pacific Biosciences (PacBio) full-length transcriptome sequencing. This dataset provided around 1.1 (WT) and 1.3 (RBM4 KO) million sequence reads of 2.6 kb average length mapping to the human genome.

2020-10-20 | GSE147896 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data