Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Optimized RiboMethSeq pipeline

ABSTRACT: Holistic optimization of bioinformatic analysis pipeline for detection and quantification of 2’-O-methylations in RNA by RiboMethSeq

PROVIDER: PRJEB35565 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3697210.fastq.gz	Fastqsanger.gz
	ERR3697211.fastq.gz	Fastqsanger.gz
	ERR3697212.fastq.gz	Fastqsanger.gz
	ERR3697213.fastq.gz	Fastqsanger.gz
	ERR3697214.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 13

Similar Datasets

Human RiboMethSeq

Project description:Human RiboMetHSeq optimization

| PRJEB34951 | ENA

RiboMethSeq of HCT116 cells treated with siCoilin

Project description:RiboMethSeq of HCT116 cells treated with siCoilin to investigate the effect of Coilin knockdown on RNA methylation as part of a larger study on the function of the protein TFIP11.

2021-09-22 | GSE179068 | GEO

RiboMethSeq of HCT116 cells treated with siTFIP11 or siDHX15

Project description:RiboMethSeq of HCT116 cells treated with siTFIP11 or siDHX15 to investigate the effect of TFIP11 or DHX15 knockdown on RNA methylation as part of a larger study on the function of TFIP11.

2021-09-22 | GSE163369 | GEO

TBpore Cluster: A Novel Phylogenetic Pipeline for Tuberculosis Transmission Studies Using Nanopore Data

Project description:TBpore Cluster bioinformatic pipeline for Mycobacterium tuberculosis phylogeny

| PRJEB77905 | ENA

RiboMethSeq of HCT116 cells treated with siCoilin

Project description:RiboMethSeq of HCT116 cells treated with siCoilin

| PRJNA742051 | 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

FTSJ1 patients RiboMethSeq

Project description:RiboMethSeq FTSJ1 tRNA Nm-MTase: new human targets and role in the regulation of brain-specific genes

| PRJEB46400 | ENA

Combined miRNA and mRNA Sequencing Identifies Protective Transcriptional Signature of Enhanced PI3Kalpha Signaling in Cardiac Hypertrophy

Project description:A molecular and bioinformatic pipeline permitting comprehensive analysis and quantification of myocardial miRNA and mRNA expression with next-generation sequencing was developed and the impact of enhanced PI3Kalpha signaling on the myocardial transcriptome signature of pressure overload-induced pathological hypertrophy was explored.

2013-05-01 | GSE35350 | GEO

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

Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples

Project description:We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and a matched hematoxylin and eosin (H&E)-stained whole slide image (WSI), optimized for Patient-Derived Xenograft (PDX) cancer specimens. Our pipeline enables the classification of sequenced transcripts for deconvolving the mouse and human species and mapping the transcripts to reference transcriptomes. We align the H&E WSI with the spatial layout of the Visium slide and generate imaging and quantitative morphology features for each Visium spot. The pipeline design enables multiple analysis workflows, including single or dual reference genomes input and stand-alone image analysis. We show the utility of our pipeline on a dataset from Visium profiling of four melanoma PDX samples. The clustering of Visium spots and clustering of H&E imaging features reveal similar patterns arising from the two data modalities.

2024-05-21 | GSE238004 | 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