Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development and application of a Ligation-based Library vs Library high- throughput Yeast Two-Hybrid (LLL-Y2H) screening system

ABSTRACT: Development and application of a Ligation-based Library vs Library high- throughput Yeast Two-Hybrid (LLL-Y2H) screening system

PROVIDER: PRJNA359495 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5136580_1.fastq.gz	Fastqsanger.gz
	SRR5136580_2.fastq.gz	Fastqsanger.gz
	SRR5136581_1.fastq.gz	Fastqsanger.gz
	SRR5136581_2.fastq.gz	Fastqsanger.gz
	SRR5136582_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Development and application of a Ligation-based Library vs Library high- throughput Yeast Two-Hybrid (LLL-Y2H) screening system

Project description:We developed a Ligation-based Library vs Library high-throughput Yeast Two-Hybrid (LLL-Y2H) screening system to explore protein interactions.

2019-12-30 | GSE93036 | GEO

Enabling multiplexed CRISPR/Cas9 screening via massively parallel in-library ligation

Project description:Here we developed a massively parallel in-library ligation methodology to simultaneously perturb four pre-designed targets in CRISPR/Cas9 screening. Thousands of pairs of sequences precisely ligated with their counterparts in library, which enabled simultaneous expression of four gRNAs from each single vector. We demonstrated this novel method with 6,236 4-gene combinations targeting 1,599 immune response related genes, and generated a plasmid library with 1,400x coverage. The library performance was evaluated in a canonical T cell activation experiment, and combinations involved in TCR signaling pathway or TCR complex were successfully identified as positive regulators. Novel combination that is reflecting a potential pathway crosstalk was also verified. This new methodology expands the capacity of the perturbation in CRISPR screening and provided a powerful tool for researches in broad fields to study the combinatorial outcomes from coordinated gene behaviors.

2022-06-15 | GSE149945 | GEO

Enabling multiplexed CRISPR/Cas9 screening via massively parallel in-library ligation

Project description:Enabling multiplexed CRISPR/Cas9 screening via massively parallel in-library ligation

| PRJNA630673 | ENA

Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system.

Project description:Protein-protein interaction (PPI) network maintains proper function of all organisms. Simple high-throughput technologies are desperately needed to delineate the landscape of PPI networks. While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still required. Here, we developed a recombination-based 'library vs library' Y2H system (RLL-Y2H), by which multi-library screening can be accomplished in a single pool without any individual treatment. This system is based on the phiC31 integrase-mediated integration between bait and prey plasmids. The integrated fragments were digested by MmeI and subjected to deep sequencing to decode the interaction matrix. We applied this system to decipher the trans-kingdom interactome between Mycobacterium tuberculosis and host cells and further identified Rv2427c interfering with the phagosome-lysosome fusion. This concept can also be applied to other systems to screen protein-RNA and protein-DNA interactions and delineate signaling landscape in cells.

| S-EPMC5815087 | biostudies-other

A novel NGS-based method can improve the efficiency and sensitivity of Y2H screening with cDNA library

Project description:The NGS-based Y2H screening methods have been adopted to increase the efficiency and sensitivity, while reducing the labor and experimental cost of the canonical Y2H screening. However, most of NGS-based Y2H screening methods are suitable for well-constructed ORFeomes but not cDNA libraries. Thus, we developed a novel NGS-based Y2H screening method to accomplish a precise Y2H screening with cDNA libraries. With newly designed primers, we can distinguish and filter out those non-in-frame reads from all mapped reads, which facilitates the estimation of the interaction intensity between baits and preys.

2021-07-09 | GSE179488 | GEO

Bias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure

Project description:High-throughput sequencing (HTS) has become a powerful tool for the detection of and sequence characterization of microRNAs (miRNA) and other small RNAs (sRNA). Unfortunately, the use of HTS data to determine the relative quantity of different miRNAs in a sample has been shown to be inconsistent with quantitative PCR and Northern Blot results. Several recent studies have concluded that the major contributor to this inconsistency is bias introduced during the construction of sRNA libraries for HTS and that the bias is primarily derived from the adaptor ligation steps; specifically where single stranded adaptors are sequentially ligated to the 3' and 5'-end of sRNAs using T4 RNA ligases. In this study we investigated the effects of ligation bias by using a pool of randomized ligation substrates, defined mixtures of miRNA sequences and several combinations of adaptors in HTS library construction. We show that like the 3' adaptor ligation step, the 5' adaptor ligation is also biased, not because of primary sequence, but instead due to secondary structures of the two ligation substrates. We find that multiple secondary structural factors influence final representation in HTS results. Our results provide insight about the nature of ligation bias and allowed us to design adaptors that reduce ligation bias and produce HTS results that more accurately reflect the actual concentrations of miRNAs in the defined starting material.

2015-05-15 | GSE67053 | GEO

Bias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure

2015-05-15 | E-GEOD-67053 | biostudies-arrayexpress

A genome-wide CRISPR library for high-throughput genetic screening in Drosophila cells

Project description:Analysis of sgRNA sequences in the raw library and at different time points after transfection into S2R+ cells Two biological repeats of all samples at three timepoints post transfection, with three dilutions of library transfected.

2015-04-01 | E-GEOD-67339 | biostudies-arrayexpress

A genome-wide CRISPR library for high-throughput genetic screening in Drosophila cells

Project description:Analysis of sgRNA sequences in the raw library and at different time points after transfection into S2R+ cells

2015-04-01 | GSE67339 | GEO

piggyBac-Mediated Genomic Integration of Linear dsDNA-Based Library for Deep Mutational Scanning in Mammalian Cells

Project description:Deep mutational scanning (DMS) makes it possible to perform massively parallel quantification of the relationship between genetic variants and phenotypes of interest. However, the difficulties in introducing large variant libraries into mammalian cells greatly hinder DMS under physiological states. Here we developed two novel strategies for DMS library construction in mammalian cells, namely ‘piggyBac-in-vitro ligation’ and ‘piggyBac-in-vitro ligation-PCR’. For the first strategy, we took the ‘in-vitro ligation’ approach to prepare high-diversity linear dsDNAs, and integrate them into the mammalian genome with a piggyBac transposon system. For the second strategy, we further added a PCR step using the in-vitro ligation dsDNAs as templates, for the construction of high-content genome-integrated libraries via large-scale transfection. Both strategies could successfully establish genome-integrated EGFP-chromophore randomized libraries in HEK293T cells and enrich the green fluorescence-chromophore amino acid sequences. And we further identified a novel transcriptional activator peptide with the ‘piggyBac-in-vitro ligation-PCR’ strategy. Our novel strategies greatly facilitate the construction of large variant DMS library in mammalian cells, and may have great application potential in the future.

2023-10-05 | GSE226719 | 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