Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types

PROVIDER: PRJNA473636 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7234630_1.fastq.gz	Fastqsanger.gz
	SRR7234630_2.fastq.gz	Fastqsanger.gz
	SRR7234640_1.fastq.gz	Fastqsanger.gz
	SRR7234640_2.fastq.gz	Fastqsanger.gz
	SRR7234650_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 164

Similar Datasets

Towards a universal sample preparation method for denaturing top-down proteomics of complex proteomes

Project description:A universal and standardized sample preparation method becomes vital for denaturing top-down proteomics (dTDP) to advance the scale and accuracy of proteoform delineation in complex biological systems. It needs to have high protein recovery, minimum bias, good reproducibility, and compatibility with downstream mass spectrometry (MS) analysis. Here we employed a lysis buffer containing sodium dodecyl sulfate (SDS) for extracting proteoforms from cells, and for the first time, compared membrane ultrafiltration (MU), chloroform-methanol precipitation (CMP), and single-spot solid-phase sample preparation using magnetic beads (SP3) for proteoform cleanup for dTDP. The MU method outperformed CMP and SP3 methods, resulting in high and reproducible protein recovery from both E. coli cell (59±3%) and human HepG2 cell (86±5%) samples without a significant bias. Single-shot capillary zone electrophoresis (CZE)-MS/MS analyses of the prepared E. coli and HepG2 cell samples using the MU method identified 821 and 516 proteoforms, respectively. Nearly 30% and 50% of the identified E. coli and HepG2 proteins are membrane proteins. CZE-MS/MS identified 94 histone proteoforms from the HepG2 sample with various post-translational modifications, including acetylation, methylation, and phosphorylation. Our results suggest that combining the SDS-based protein extraction and the MU-based protein cleanup could be a universal sample preparation method for dTDP.

2020-05-22 | PXD018248 | Pride

Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics based on Acid Extraction

Project description:We report a universal detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types. The protocol is highly reproducible, virtually loss-less and enables very rapid sample processing. SPEED is superior to detergent/chaotropic agent-based methods for quantitative proteomics and enhances proteome coverage for challenging samples.

2019-11-25 | PXD011189 | Pride

human gut metagenome

Project description:Method assessment of fecal DNA extraction

| PRJDB6503 | ENA

DNA extraction method from alfalfa

Project description:DNA extraction method from alfalfa Metagenome

| PRJNA901244 | ENA

DNA_nanocellulose

Project description:DNA extraction method for mineral samples

| PRJEB61213 | ENA

DNA Extraction

Project description:DNA extraction method targeted loci environmental

| PRJNA315949 | ENA

A high-throughput ancient DNA extraction method for large-scale sample screening

Project description:A high-throughput ancient DNA extraction method for large-scale sample screening

| PRJEB82618 | ENA

Three-in-one simultaneous extraction of proteins, metabolites and lipids for multi-omics

Project description:Elucidation of complex molecular networks requires integrative analysis of molecular features and changes at different levels of information flow and regulation. Accordingly, high throughput functional genomics tools such as transcriptomics, proteomics, metabolomics and lipidomics have emerged to provide system-wide investigations. Unfortunately, analysis of different types of biomolecules requires specific sample extraction procedures in combination with specific analytical instrumentation. The most efficient extraction protocols often only cover a restricted type of biomolecules due to their different physicochemical properties. Therefore, several sets/aliquots of samples are needed for extracting different molecules. Here we adapted a bi-phasic fractionation method to extract proteins, metabolites and lipids from the same sample (3-in-1) for liquid chromatography-tandem mass spectrometry (LC-MS/MS) multi-omics. To demonstrate utility of the improved method, we used bacteria-primed Arabidopsis leaves to generate multi-omics datasets from the same sample. In total, we were able to analyze 1849 proteins, 1967 metabolites and 424 lipid species in single samples. The molecules cover a wide range of biological and molecular processes. Our results have shown the clear advantages of the multi-omics method, including sample conservation, high reproducibility and tight correlation between different types of biomolecules.

2021-08-17 | PXD023094 | Pride

Method DNA extraction Mars simulant soil

Project description:DNA extraction method for synthetic Mars soil

| PRJEB68335 | ENA

A Universal 384-Well Proteomic Sample Preparation Platform for High-Throughput Screening and Biomarker Discovery

Project description:Major advances have been made to develop an automated universal 384-well plate sample preparation platform with high reproducibility and adaptability for extraction of proteins from cells within a culture plate. An in-solution digest strategy is employed to generate peptides from the extracted proteins for LC-MS analysis in the 384-well plate. Method evaluation utilized HeLa cells cultured in the 384-well plate ranging from 500 – 10,000 cells. Digestion efficiency was excellent in comparison to the commercial digest peptides standard with minimal sample loss while improving sample preparation throughput by 20 – 40 fold. Analysis of six human cell types, which included two primary cell samples identified and quantified approximately 4,000 proteins for each sample in a single LC-MS/MS injection with as little as 100 – 10,000 cells depending on cell type demonstrating universality of the platform. Implementation of the comprehensive 384-well format protocol for processing cells to clean digested peptides enables large-scale biomarker validation and compound screening through proteomic analysis.

2021-06-14 | PXD019733 | Pride

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