Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay

ABSTRACT: Multi-modal single-cell assays provide high-resolution snapshots of complex cell populations but are mostly limited to transcriptome plus an additional modality. Here, we describe Expanded CRISPR-compatible Cellular Indexing of Transcriptomes and Epitopes by sequencing (ECCITE-seq) for the high-throughput characterization of at least five modalities of information from each single cell. We demonstrate application of ECCITE-seq to multimodal CRISPR screens with robust direct sgRNA capture and to clonotype-aware multimodal phenotyping of cancer samples.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE126310 | GEO | 2019/03/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay

Project description:Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay

| PRJNA521522 | ENA

Stereotypic persistent B cell receptor clonotypes in Alzheimer’s Disease

Project description:The growing evidence suggest that the effect of Alzheimer’s Disease (AD) is not solely restricted to the brain. Numerous groups investigated the relation between the central nervous system and peripheral system, whereupon the peripheral system is closely involved in accordance with the progression of disease and systemic immunity. In our previous report, we identified shared B cell receptor (BCR) sequences among 10 AD patients which showed similar class-switching orientation, identical isotypes and high somatic hypermutation rate. For further investigation, we recruited 44 patients with AD at baseline and 37 patients for second follow-up to identify the shared BCR sequences among patients and persistent BCR within an individual patient. We were able to annotate 3983 unique AD specific BCR clonotypes and one of the clonotype showed binding affinity against human Aβ42 peptide. Our finding can provide evidence of common BCRs in AD patients exposed to antigenic stimulus which are related to AD pathogenesis.

2023-09-13 | GSE242738 | GEO

Simultaneous measurements of auto-immune and infectious disease specific antibodies using a high throughput multiplexing tool.

Project description:Considering importance of ganglioside antibodies as biomarkers in various immune-mediated neuropathies and neurological disorders, we developed a high throughput multiplexing tool for the assessment of gangliosides-specific antibodies based on Biolpex/Luminex platform. In this report, we demonstrate that the ganglioside high throughput multiplexing tool is robust, highly specific and demonstrating ?100-fold higher concentration sensitivity for IgG detection than ELISA. In addition to the ganglioside-coated array, the high throughput multiplexing tool contains beads coated with influenza hemagglutinins derived from H1N1 A/Brisbane/59/07 and H1N1 A/California/07/09 strains. Influenza beads provided an added advantage of simultaneous detection of ganglioside- and influenza-specific antibodies, a capacity important for the assay of both infectious antigen-specific and autoimmune antibodies following vaccination or disease. Taken together, these results support the potential adoption of the ganglioside high throughput multiplexing tool for measuring ganglioside antibodies in various neuropathic and neurological disorders.

| S-EPMC3431397 | biostudies-other

HDX-MS of AcrIF9 and AcrIF2 binding to CRISPR IF Csy complex

Project description:CRISPR RNA-guided detection and degradation of foreign DNA is a dynamic process. Viruses can interfere with this cellular defense by expressing small proteins called anti-CRISPRs. While structural models of anti-CRISPRs bound to their target complex provide static snapshots that inform mechanism, the dynamics and thermodynamics of these interactions are often overlooked. Here we use hydrogen deuterium exchange-mass spectrometry (HDX-MS) and differential scanning fluorimetry (DSF) experiments to determine how anti-CRISPR binding impacts the conformational landscape of the type IF CRISPR RNA guided surveillance complex (Csy) upon binding of two different anti-CRISPR proteins (AcrIF9 and AcrIF2). The results demonstrate that AcrIF2 binding relies on enthalpic stabilization, whereas AcrIF9 uses an entropy driven reaction to bind the CRISPR RNA-guided surveillance complex. Collectively, this work reveals the thermodynamic basis and mechanistic versatility of anti-CRISPR-mediated immune suppression. More broadly, this work presents a striking example of how allosteric effectors are employed to regulate nucleoprotein complexes.

2022-11-01 | PXD036446 | Pride

Expanding the Scope of Bacterial CRISPR Activation with PAM-flexible dCas9 Variants

Project description:CRISPR-Cas transcriptional tools have been widely applied for programmable regulation of complex biological networks. In comparison to eukaryotic systems, bacterial CRISPR activation (CRISPRa) has stringent target site requirements for effective gene activation. While genes may not always have an NGG protospacer adjacent motif (PAM) at the appropriate position, PAM-flexible dCas9 variants can expand the range of targetable sites. Here we systematically evaluate a panel of PAM-flexible dCas9 variants for their ability to activate bacterial genes. We observe that dxCas9-NG provides a high dynamic range of gene activation for sites with NGN PAMs while dSpRY permits modest activity across almost any PAM. Similar trends were observed for heterologous and endogenous promoters. For all variants tested, improved PAM-flexibility comes with the tradeoff that CRISPRi-mediated gene repression becomes less effective. Weaker CRISPR interference (CRISPRi) gene repression can be partially rescued by expressing multiple sgRNAs to target many sites in the gene of interest. Our work provides a framework to choose the most effective dCas9 variant for a given set of gene targets, which will further expand the utility of CRISPRa/i gene regulation in bacterial systems.

2022-11-15 | GSE217559 | GEO

CRISPR-based multimodal genetic screens in human iPSC-derived neurons

Project description:CRISPR-based multimodal genetic screens in human iPSC-derived neurons

| PRJNA513160 | ENA

Expanding the genetic tool kit helps dissect a global stress response in the early-branching species Fusobacterium nucleatum

Project description:We elucidated the global regulatory network of sigma E in Fusobacterium nucleatum. For this, we developed new genetic tools for the anaerobic bacterium. This uncovered a conserved regulon of the sigma factor including a noncoding arm of the sRNA FoxI. In this process, FoxI serves as a negative regulator of sigma E to downregulate several outer membrane proteins as well as the putative galactose transporter mglBAC.

2022-09-20 | GSE192339 | GEO

Single cell sequencing for B cell repertoire of multi-year serial blood samples from a healthy donors.

Project description:Transcriptional and clonotype analysis aimed at investigation of the structure, stability and dynamics of the human memory B cell pool, using peripheral blood samples collected from a single healthy donor with an interval of 4 years.

2022-05-14 | E-MTAB-11697 | biostudies-arrayexpress

Single cell sequencing for B cell repertoire of multi-year serial blood samples from two healthy donors.

Project description:Transcriptional and clonotype analysis aimed at investigation of the structure, stability and dynamics of the human memory B cell pool, using peripheral blood samples collected from two healthy donors with an interval of 10 or 6 years.

2022-04-26 | E-MTAB-11174 | biostudies-arrayexpress

CRISPRTE: A web-based tool to generate single guide RNA targets transposable elements

Project description:CRISPR/Cas systems have gained prominence as powerful tools for genome engineering. Recent investigations into the crucial role of transposable elements (TEs) have stimulated research interest in manipulating TEs to elucidate their functions. Nevertheless, designing single guide RNAs (sgRNAs) that are both specific and efficient for TE manipulation presents a formidable challenge, considering the repetitive nature and high copy numbers of TEs. Although various sgRNA design tools have been developed for gene editing, an optimized sgRNA designer explicitly for TE manipulation has yet to be established. To bridge this gap, we presented CRISPR-TE, a web-based application featuring an accessible graphical user interface, available at https://www.crisprte.cn. CRISPR-TE could identify all potential sgRNAs for TEs and offers a comprehensive solution for efficient TE targeting at both the single duplicate and subfamily levels. We also demonstrated that young TEs can be targeted with higher coverage at the subfamily level. Finally, we validated the overexpression of SVAD, a human-specific TE, using dCas9-VP64 activator incorporated with three sgRNAs designed by our tool. Collectively, our findings suggest that CRISPR-TE may serve as a versatile framework for designing sgRNAs aimed at TE targeting.

2024-03-24 | GSE228266 | 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