Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: probe-captured AIRR sequencing

PROVIDER: PRJNA767687 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR16172988_1.fastq.gz	Fastqsanger.gz
	SRR16172988_2.fastq.gz	Fastqsanger.gz
	SRR16172989_1.fastq.gz	Fastqsanger.gz
	SRR16172989_2.fastq.gz	Fastqsanger.gz
	SRR16172990_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Seven chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes

Project description:In rheumatoid arthritis (RA), the activation of T and B cell clones specific for self-antigens leads to the chronic inflammation of the synovium. Here, we perform an in-depth quantitative analysis of the seven chains that comprise the adaptive immune receptor repertoire (AIRR) in RA. In comparison to controls, we show that RA patients have multiple and strong differences in the BCR repertoire including reduced diversity as well as altered isotype, chain and segment frequencies. We demonstrate that therapeutic TNF inhibition partially restores this alteration but find a profound difference in the underlying biochemical reactivities between responders and non-responders. Combining the AIRR with HLA typing, we identify the specific TCR repertoire associated with disease risk variants. Integrating these features, we further develop a molecular classifier that shows the utility of the AIRR as a diagnostic tool. Simultaneous sequencing of the seven chains of the human AIRR reveals novel features associated with the disease and clinically relevant phenotypes, including response to therapy. These findings show the unique potential of AIRR to address precision medicine in immune-related diseases.

2024-02-23 | GSE256256 | GEO

CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq) (HEK293T MCF7)

Project description:CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq) (HEK293T MCF7)

| PRJNA526737 | ENA

Targeted RNA sequencing for gene discovery and quantification

Project description:Due to the large size, complex splicing and wide dynamic range of eukaryotic transcriptomes, RNA sequencing samples the majority of expressed genes infrequently, resulting in sparse sequencing coverage that can hinder robust isoform assembly and quantification. Targeted RNA sequencing addresses this challenge by using oligonucleotide probes to capture selected genes or regions of interest for focused sequencing. This enhanced sequencing coverage confers sensitive gene discovery, robust transcript assembly and accurate gene quantification. Here we describe a detailed protocol for all stages of targeted RNA sequencing, from initial probe design considerations, capture of targeted genes, to final assembly and quantification of captured transcripts. Initial probe design and final analysis can take less than a day, while the central experimental capture stage requires ~7 days.

2014-03-01 | GSE52503 | GEO

Homo sapiens

Project description:AIRR test

| PRJNA412229 | ENA

Well-ST-seq: cost-effective and cellular level spatial transcriptomics with high RNA capture efficiency

Project description:Spatial transcriptomic technologies are promising tools to reveal fine anatomical profiles of tissues. In the case of methodologies utilizing barcoded probe arrays, achieving a balance among probe barcoding complexity, cost, gene capture sensitivity, and spatial resolution is crucial for accelerating the spreading speed of spatial transcriptomic in basic science and clinical work. Here, we developed spatially cellular-level RNA-capture probe arrays using miniaturized microfluidic and microarray technologies. By leveraging the predetermined and cost-effective probe fixation characteristics of this methodology, we significantly reduced the consumable cost of the probe array to $0.31/mm2 and fabrication time to approximately 2 hours. Furthermore, the modification of the RNA-capture probe on sequencing slides by microfluidic chip does not rely on large imaging or printing instruments. Notably, the efficiency of the transcript captured by the probe array is even comparable to conventional single-cell RNA sequencing. Based on this technology, the stacked three-dimensional transcriptome atlas and the spatial cell heterogeneity of mouse brains were successfully visualized. Taken together, we present an experimental and analytical framework for the spatial investigation of mouse brain structures and cell phenotypes.

2024-05-01 | GSE247834 | GEO

Targeted RNA sequencing for gene discovery and quantification

2014-03-01 | E-GEOD-52503 | biostudies-arrayexpress

Control and LgG4 binding proteins

Project description:Proteins were captured with monosaccharide(Control) and LgG4 probe. Resulting proteins were went through proteomics. Unique proteins found in LgG4 samples were selected for further research.

2024-04-30 | PXD030528 | Pride

CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq) (HEK293T MCF7)

Project description:The CDKN2A/B locus at 9p21.3 contains crucial tumor suppressors (P16, P14, and P15) and oncogenic lncRNA ANRIL genes. This locus is most frequently inactivated in cancer genomes by deletion and DNA methylation. However, the mechanisms coordinately regulating their expression level are far from clear. In the present study, a novel lncRNA, P14AS, was characterized in the antisense strand of the fragment near CDKN2A in human cell lines using CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq).

2019-03-13 | GSE128205 | GEO

Oncogenic Antisense LncRNA P14AS Regulates Expression of ANRIL through AUF1 Binding

Project description:The CDKN2A/B locus at 9p21.3 contains crucial tumor suppressor (P16, P14, and P15) and oncogenic lncRNA ANRIL genes. This locus is most frequently inactivated in cancer genomes by deletion and DNA methylation. However, the mechanisms coordinately regulating their expression level are far from clear. In the present study, a novel lncRNA, P14AS, was characterized in the antisense strand of the fragment near CDKN2A exon1 in human cell lines using CDKN2A-specific probe captured RNA-sequencing (RNACap-Seq).

2019-03-07 | GSE127905 | GEO

Nanostring based analysis of CBF-AML patients

Project description:miR-130a is captured as part of a 798 gene probe set on a microarray plate for 48 CBF patients In the group of patients defined here, survival characteristics and relapse information was collected to unbiasedly assess the impact of any miRNA on survival

2022-03-08 | GSE196177 | 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