Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

One-pot method for preparing DNA, RNA, and protein for multiomics analysis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE241434 | GEO | 2024/03/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

One-pot method for preparing DNA, RNA, and protein for multiomics analysis II

Project description:Typical multiomics studies employ separate methods for DNA, RNA, and protein sample preparation, which is labor intensive, costly, and prone to sampling bias. We describe a method for preparing high-quality, sequencing-ready DNA and RNA, and either intact proteins or mass-spectrometry-ready peptides for whole proteome analysis from a single sample. This method utilizes a reversible protein tagging scheme to covalently link all proteins in a lysate to a bead-based matrix and nucleic acid precipitation and selective solubilization to yield separate pools of protein and nucleic acids. We demonstrate the utility of this method to compare the genomes, transcriptomes, and proteomes of four triple-negative breast cancer cell lines with different degrees of malignancy. These data show the involvement of both RNA and associated proteins, and protein-only dependent pathways that distinguish these cell lines. We also demonstrate the utility of this multiomics workflow for tissue analysis using mouse brain, liver, and lung tissue.

2024-03-08 | GSE241433 | GEO

One-pot method for preparing DNA, RNA, and protein for multiomics analysis I

2024-03-08 | GSE241432 | GEO

One-pot method for preparing DNA, RNA, and protein for multiomics analysis

Project description:One-pot method for preparing DNA, RNA, and protein for multiomics analysis

| PRJNA1008152 | ENA

One-pot method for preparing DNA, RNA, and protein for multiomics analysis II

Project description:One-pot method for preparing DNA, RNA, and protein for multiomics analysis II

| PRJNA1008155 | ENA

One-pot method for preparing DNA, RNA, and protein for multiomics analysis I

Project description:One-pot method for preparing DNA, RNA, and protein for multiomics analysis I

| PRJNA1008156 | ENA

Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments.

Project description:In the era of synthetic biology, techniques for rapidly constructing a designer long DNA from short DNA fragments are desired. To realize this, we attempted to establish a method for one-step DNA assembly of unprecedentedly large numbers of fragments. The basic technology is the Ordered Gene Assembly in Bacillus subtilis (OGAB) method, which uses the plasmid transformation system of B. subtilis. Since this method doesn't require circular ligation products but needs tandem repeat ligation products, the degree of deviation in the molar concentration of the material DNAs is the only determinant that affects the efficiency of DNA assembly. The strict standardization of the size of plasmids that clone the DNA block and the measurement of the block in the state of intact plasmid improve the reliability of this step, with the coefficient of variation of the molar concentrations becoming 7%. By coupling this method with the OGAB method, one-step assembly of more than 50 DNA fragments becomes feasible.

| S-EPMC4438487 | biostudies-literature

Preparing for the first breath at single cell level

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-01-06 | GSE122332 | GEO

MARIS: Method for Analyzing RNA following Intracellular Sorting

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-01-17 | E-GEOD-54179 | biostudies-arrayexpress

Phosphorylation of an HP1-like protein regulates RNA-bridged heterochromatin body assembly for DNA elimination

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-12-10 | E-GEOD-70083 | biostudies-arrayexpress

Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes.

Project description:We have developed a protocol to assemble in one step and one tube at least nine separate DNA fragments together into an acceptor vector, with 90% of recombinant clones obtained containing the desired construct. This protocol is based on the use of type IIs restriction enzymes and is performed by simply subjecting a mix of 10 undigested input plasmids (nine insert plasmids and the acceptor vector) to a restriction-ligation and transforming the resulting mix in competent cells. The efficiency of this protocol allows generating libraries of recombinant genes by combining in one reaction several fragment sets prepared from different parental templates. As an example, we have applied this strategy for shuffling of trypsinogen from three parental templates (bovine cationic trypsinogen, bovine anionic trypsinogen and human cationic trypsinogen) each divided in 9 separate modules. We show that one round of shuffling using the 27 trypsinogen entry plasmids can easily produce the 19,683 different possible combinations in one single restriction-ligation and that expression screening of a subset of the library allows identification of variants that can lead to higher expression levels of trypsin activity. This protocol, that we call 'Golden Gate shuffling', is robust, simple and efficient, can be performed with templates that have no homology, and can be combined with other shuffling protocols in order to introduce any variation in any part of a given gene.

| S-EPMC2677662 | biostudies-literature

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