Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MP3-seq: Massively parallel measurement of protein-protein interactions by sequencing

ABSTRACT: MP3-seq: Massively parallel measurement of protein-protein interactions by sequencing

PROVIDER: PRJNA1133167 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR29760751_1.fastq.gz	Fastqsanger.gz
	SRR29760751_2.fastq.gz	Fastqsanger.gz
	SRR29760752_1.fastq.gz	Fastqsanger.gz
	SRR29760752_2.fastq.gz	Fastqsanger.gz
	SRR29760753_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 68

Similar Datasets

MP3-seq: Massively parallel measurement of protein-protein interactions by sequencing

Project description:Abstract: Protein-protein interactions (PPIs) regulate many cellular processes, and engineered PPIs have cell and gene therapy applications. Here we introduce massively parallel protein-protein interaction measurement by sequencing (MP3-seq), an easy-to-use and highly scalable yeast-two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs, and barcode enrichment can be read by sequencing to provide a direct measure of interaction strength. We show that MP3-seq is highly quantitative and scales to over 100,000 interactions. We apply MP3-seq to characterize interactions between families of rationally designed heterodimers and to investigate elements conferring specificity to coiled-coil interactions. Finally, we predict coiled heterodimer structures using AlphaFold-Multimer (AF-M) and train linear models on physics simulation energy terms to predict MP3-seq values. We find that AF-M-based models could be valuable for pre-screening interactions, but that measuring interactions experimentally remains necessary to rank their strengths quantitatively.

2024-07-12 | GSE271790 | GEO

Massively Parallel Dissection of RNA in RNA-protein Interactions in vivo

Project description:Massively Parallel Dissection of RNA in RNA-protein Interactions in vivo

| PRJNA914866 | ENA

Massively Parallel Dissection of RNA in RNA-protein Interactions in vivo

Project description:Many of the biological functions performed by RNA are mediated by RNA-binding proteins (RBPs), and understanding the molecular basis of these interactions is fundamental to molecular biology. Here, we present MPRNA-immunoprecipitation (MPRNA-IP), an adaptation of the previously developed massively parallel RNA assay (MPRNA) for in vivo high-throughput dissection of RNA-protein interactions, and describe statistical models for identifying RNA domains and parsing the structural contributions of RNA. By using custom pools of tens of thousands of RNA sequences containing systematically designed truncations and mutations, we are able to identify RNA domains, sequences, and secondary structures necessary and sufficient for protein binding in a single experiment. We show that this approach is successful for multiple RNAs of interest including NORAD, MS2, and human telomerase RNA, and we use it to interrogate the RNA-binding preferences of the DNA-looping factor CTCF. By blending modern and classical approaches, MPRNA-IP provides a novel high-throughput way to elucidate RNA-based mechanisms behind RNA-protein interactions.

2024-04-15 | GSE221537 | GEO

Mapping of copy-number alterations with massively parallel sequencing

Project description:This SuperSeries is composed of the following subset Series: GSE12019: Fine-scale mapping of copy-number alterations with massively parallel sequencing GSE13372: High-resolution mapping of copy-number alterations with massively parallel sequencing Refer to individual Series

2008-11-13 | E-GEOD-13373 | biostudies-arrayexpress

Massively parallel engineering of persistent CAR-Ts

Project description:Massively parallel engineering of persistent CAR-Ts

| PRJNA906963 | ENA

Massively parallel engineering of persistent CAR-Ts

Project description:Massively parallel engineering of persistent CAR-Ts

| PRJNA833968 | ENA

Massively parallel engineering of persistent CAR-Ts [CLASH]

Project description:Massively parallel engineering of persistent CAR-Ts [CLASH]

| PRJNA853858 | ENA

Massively parallel engineering of persistent CAR-Ts [GEO_CLASH_Integration_off_targets]

Project description:Massively parallel engineering of persistent CAR-Ts [GEO_CLASH_Integration_off_targets]